I have been photographing wild flowers since 2002. In that time I have taken perhaps 80,000 digital photos of wild flower plants, using a variety of cameras. So I may have garnered a little experience at the task.
For this reason, and others, I prefer to use a small compact with rear LCD panel. Six mega-pixels is easily sufficient; take a look at the examples shown to see for yourself. There are models around that will take near-macro shots (without approaching to within 1cm of the flower!) and are fast enough to be ready to take a photograph within a second of switch-on, will take 3 exposure-bracketed shots in the space of another two seconds, and are free to take another 3 shots in yet another couple. There are other models that are so slow to switch-on, so ponderous at taking bracketed exposures, and downright dilatory at being ready to take another three shots; so chose your model with care. Remember, if you are taking hand-held photos of swaying flowers, then the faster the photographs are taken, the less time there is for the flower (or you) to move out of frame or out of focus.
With a compact camera being so thin (about 1cm), it is also possible to sneak the lens underneath the umbrella of mushrooms and likewise other low plants. You couldn't do likewise with an SLR unless you used something like a dentists' mirror.
Bridge-type cameras don't suffer from some of the disadvantages of SLR-type cameras. In particular, they almost invariably have a swinging LCD panel that enables ground-level shots without grovelling on the ground and they are usually lighter, and perhaps even usable single-handed over water.
Some disadvantages to using a (good) compact digicam are that the contrast is usually fairly high, and noise at higher ISO 'film-speeds' settings can become a distraction. Also, at wide apertures (low f/numbers) the aperture may be more square than round leading to a pronounced rectangular bokeh (out of focus picture elements). A good compromise is to use both an SLR type and a compact, which is what I do.
Photographing wild flowers can be a tricky business. Usually they are surrounded by other plants, so a careful 'weeding' process may become necessary to isolate it from its surroundings before attempting to photograph them. But be careful not to weed the plant you are trying to photograph! And never weed around rare plants. Try a different approach angle instead.
On some cameras the focal point setting can be usefully fixed to one particular spot in the frame. This then ensures that you consistently know where in the frame the camera is going to try to focus. I set my camera to focus in the centre of the frame and do not allow the camera to chose its own focus spot, as that is invariably not where the flower/subject is!
First make sure that if your camera has a macro setting, that you un-set that macro setting. Focussing may well take longer on macro setting because the lens has to rack out and back much further.
For a mostly airy plant (like Wall Lettuce, for example), automatic focussing can be troublesome. I find it useful to either place a hand (or a patterned card, that is not mostly white) in the same plane as the plant, and focus on that. An alternative strategy is to point the lens at the base of the plant, where it cannot focus on anything but the plant or the ground around the base of the plant, then tilt the camera back a bit, also backing the camera away slightly to compensate for the slight difference between the hypotenuse and the adjacent focussing distances.
If there is a wall directly behind the plant, this can help with focussing, as the camera cannot focus on anything further away than the wall. Assuming it has focussed on the wall (as is likely) and not the plant, move the camera backwards the same distance that the plant is away from the wall.
If your camera refuses to focus, then you could be too near the subject. Try backing off a little. Or, it could be too dark for the focussing to work, or there may be in-sufficient contrast in the part of the image upon which the camera is focusing. Or you may have zoomed the lens and now it cannot focus as close as when it is not zoomed.
With some compact cameras, the camera lens will find focus much easier on a thin and slender plant stalk when the camera is held horizontally than it will with the same camera held vertically. This is due to the orientation of the focussing pixels in the camera. Better cameras will not be subject to this unwanted phenomenon.
I find that digital cameras get the exposure more often correct if the cameras' auto-exposure setting is set to under-expose by about 2/3rds of a stop - this is because most cameras automatically assume you are going to get some sky in the photo - and if you are pointing it at the ground, then you will get no sky in it and the camera may then over-expose the image because it is set up to expect sky. I also find that you are more likely to get a good exposure if the camera is also set to automatically bracket the exposure by about 2/3rds of a stop. Doing this will result in three exposures, one of -4/3rds another at -2/3rds and the third at a nominal -0 stops. One of these will hopefully result in a good exposure, without any over-exposure anywhere. Different cameras may well vary. It is best to experiment with your own camera; after all, you are not wasting any film.
A high shutter speed will help reduce motion blur, but will not help much with the framing when the plant sways out-of-frame. A responsive camera (one that has as short a shutter-lag as possible) helps enormously. A camera that takes ages to take the photograph after pressing the shutter button is usually a waste of time (and money). Automatic focussing can consume some of this time, but pressing the shutter button half-way will usually pre-set the focus.
What is not generally appreciated in the day of the digital camera age with many differing formats (most sensors are not 35mm film sized (24mm x 36mm) but all sorts of shapes and sizes, many a great deal smaller than even 'half-frame' (24mm x 18mm) is that the depth of field varies with sensor size (all other things being equal). A fingernail-sized sensor has a much greater depth of field (filling the frame with the required image at the same aperture) than does a larger sensor. You gain depth of field by having a smaller sensor. This gives compact cameras an advantage over full-frame cameras, which, in order to get the same depth of field, would have to set a much narrower aperture (higher f/number). There is, of course, a trade-off, smaller sensors have higher pixel noise. But small-format cameras can offset this higher noise to some extent; the image is brighter because the aperture can be set much wider (small f/number) and a higher shutter speed can be used to counteract movement.
To obtain a good depth of field usually requires an aperture smaller than f/8 on a full-frame camera (or f/2.8 on a much smaller sized sensor). But diffraction can start reducing the resolution beyond about f/16 on a full-frame camera (or at or above about f/5.6 on a much smaller sensor). To pick out a small detail by blurring others surrounding it requires a small aperture, maybe f/4 or smaller. But a great deal depends upon the focal length that is set, and the camera to subject distance. There is no hard and fast rule of thumb (well, there is, but it is not easy to apply in the field). If in doubt, try several settings. After all, the plant may have died or been trampled by next week, and it may be the only specimen for miles. To see another may take hundreds of miles of trekking as well as a wait until next year. And even if you were to come back to the exact same spot next year (assuming you can remember where that was) and at the same time of year, you may find that the plant has failed to re-grow! There have been many instances where that has happened to myself. The motto is to take the photo while you can.
To help get correct exposure there is usually a flash exposure compensation adjustment (which can be entirely separate from the non-flash exposure compensation adjustment). This may have to be set to -1/2, -1 stop, or even -1 1/2 stops. This can only be set be a little experimentation. Once set to a negative flash exposure-compensation value, small variations in subject distance will often be sufficient to get a good exposure (due to inverse-square law). So take a few photos at varying distances using the same flash exposure compensation.
Using all your senses (those not captured by a photograph) is also sometimes necessary for identification. For instance, are the leaves soapy to the touch, does the plant feel sticky, does the plant respond to touch by moving, do the seed pods explode when disturbed, does the flower smell (of what?), does the plant taste or is it tasteless (eating any part of a plant is not something which should be done unless you are certain that the plant is not deadly poisonous), do the leaves smell when crushed (of what), do the seeds stick to clothing, etc.
I, on a mountain hike, do not usually have the time to identify the plant using a book on the spot there and then, so I have to make sure I photograph every aspect of the plant so that I am hopefully able to identify the plant on the computer afterwards using several books. Sometimes I realise that because I haven't got a clear picture of some vital aspect of the plant, absolute identification is now impossible. Pity, but I cannot use such an image on my website without identification.
However, you have to draw the line somewhere. There are about 250 differing dandelions, and only dandelion experts with microscopes and biological laboratories can differentiate between them. Likewise with eyebrights and hawkweeds and several other plants. Such plants are usually grouped together under a single name in books, and only a brief mention is made of the possible number of variants and the extreme difficulty of non-expert discrimination between them.
An example of a file usefully named would be:
Where the major plant name comes first and the adjective plant name (if there is one) is enveloped within round brackets. Naming the plant this way ensures that all plants with the same 'surname' e.g Anemone(Balkan), Anemone(Blue), Anemone(Wood) and Anemone(Yellow) are all grouped together and in alphabetical order when listed on a computer. I also use initial capitalisation to help visibility and readability, especially when words are concatenated together without underscores '_' between them, as in 'NewBrighton'. Concatenating words and using initial capitalisation helps reduce filename length, which is at a premium on a computer.
The year (in 4 digits to help historians or your relatives in the succeeding centuries) precedes the month (in numbers using two digits, including a leading zero for the first 9 months) which precedes the day number (also using 2 digits). The location I put next, followed by the incremental index number (using three digits, with leading zeros as padding if necessary) - which allows you up to 999 photos in one day (use 4 digits if you take up to 9999 photos in one day).
Finally, the filename extension, just use '.jpg' rather than waste an un-necessary extra character with '.jpeg'.
Use underscores as phrase separators, but not as word-separators. Again, this is to help reduce filename length. An example night be:
to quote a contrived combination.
Do not use hard spaces (ASCII character 160) anywhere in the filename, as the file cannot then be used on a website without modifying the filename first. The same goes for any other characters you might get away with on your particular computer, but which websites cannot tolerate. Use only round brackets (), square brackets  and underscores _. In particular do not use colons, commas, question marks or any other non-alphanumeric symbols in the filename. This also helps with transferring files to any other operating system, such as Linux, Unix, AppleMac, RiscOS, etc, etc. Each operating system has differing alphanumeric characters which are disallowed in filenames. Do not make it hard for yourself to switch computers or share files with friends: use only a very limited set of characters in filenames.
The date and index number also makes each file unique, ensuring one will never over-write another even after mixing many files up together. Putting the plant name first ensures that all the same plants will all congregate together when the files are sorted alphabetically.
You could store all your Avens together in a directory named Avens, as do I. This makes the file list much less cumbersome, and greatly speeds access.
Whatever naming system you adopt or devise, be methodical. Don't leave them as PICT9856.JPG, which is both meaningless, and moreover will not be unique when you take more than 10,000 photos!
For holiday photos I omit the leading flower name, making the date the foremost item in the filename. By using exactly (and always) 10 characters for the date (with leading zeros as padding, if necessary) and always putting the year first, followed by the month number followed by the date ensures that alphabetic sorting will also result in date sorting. The best of both worlds! Example below.
I reject those images where no part of the image (due to over-exposure, blurring or under-exposure) can be salvaged for some use.
For my Wild Flower website, I have standardised on a width of 580 pixels for the processed picture (the height is variable, being dependent upon aspect ratio, which I never allow to be anything other than 1:1 (vertical:horizontal scales).
I do not take the digicam photos at this resolution, but always use the maximum resolution of the camera. This enables me to crop the images as I see fit to try and eliminate other encroaching plants, or to exclude those parts of the wanted plant that are out of focus. Using full resolution images as my source enables me to selectively pick out certain aspects of a plant at full-scale. For wider views of the plants I may reduce the image size (with 'keep aspect ratio' set, and horizontal resolution set to 580 pixels). Thus I may use the same photograph more than once on the website.
The images may need tweaking with respect to histogram, brightness, contrast, gamma, and finally a slight sharpening.
They are then ready for putting in the website; a laborious process, but now made that little bit easier by in-house written bespoke software.