I know that when doing much macro work that the autofocus system is nearly useless. When hand holding and trying to manually focus, I find myself continually going a little too far or just not far enough. The distances involved are so tiny that nearly any movement drastically changes the focus.
Are there techniques to help get macro shots in better focus? It seems like I end up with like a 10:1 ratio of out-of-focus:in-focus shots currently.
Other than the obvious ways to increase depth of field - narrower aperture (with higher ISO if necessary), shorter focal length - what I sometimes do is set the camera to continuous shooting mode and move slowly towards or away from the subject while shooting. Trying this a few times will hopefully yield at least one sharp photo.
Back in the old pre-electronic, pre-digital days, I traveled widely with a beautiful 100mm macro lens: manual focus, manual exposure (but in-camera exposure sensing). When time and opportunity permits, and the subject is stable, manually focusing on a tripod mount works fine. (This doesn't work even with slowly moving subjects: you'll find yourself constantly picking up and repositioning the tripod, which becomes just so much dead weight.) For quick photos, moving subjects, or in difficult spots, the trick is to set the focus and simply move the camera forward and back until the subject is in focus. The depth of field often is just a couple millimeters or less, so you have to be precise and steady, but it doesn't take much practice to do it reasonably well. The ability to get a depth-of-field preview is extremely useful here. A good, bright focusing screen is also quite helpful.
I'm sure the fire-a-burst-of-shots technique can help, but I cannot remember any picture (out of thousands) that I lost because of lack of focus and I certainly didn't have any burst capability. That's probably selective memory and age catching up with me, but I don't think I'm that forgetful :-). The vibrations set up by a fast series of shots, coupled with your loss of view in the viewfinder, could actually make the burst technique less reliable then getting off one shot when everything is just right.
This detail from a scanned negative gives a sense of how rapidly the focus blurs with distance: compare the berry stems to the berries themselves. The depth of field is about 3 mm. It was simultaneously focused and composed by moving the camera.
I stand with one foot in front of the other, set the focus as close as possible, then rock back and forth, weight most on the front foot, and click off 3-4 shots at a time. From what I've read, this seems to be the most common technique. Take a deep breath, get close, rock and fire off a bunch of shots.
If I'm near 1:1, I try to use f/8 or f/11 since DOF is so small anyway. I bump up the ISO to 800 if necessary and pop in some flash to get the fastest shutter speed possible, since camera shake is very noticeable at such close distances.
As dpollitt suggested, you can focus stack. If you use photoshop, load 2 or more images into layers and use edit > autoblend - it does a very good job at picking the sharpest bits of each image layer.
This is probably too short for a real answer, but I'll throw it in anyways. Try focus bracketing, where you simply shoot multiple images at different focus points. I start with what I think is in focus, then reach back slightly, and shoot 3-5 images to extend past where I think the focus is. Sorry I know this is a no brainer for most:)
Another thing that may assist is using half of the "focus stacking" technique. Where instead of combining the resulting images, you simply select the one that best suits the focus you wanted to achieve. You could even use software such as DSLR Remote Pro to do the focus bracketing automatically(if you have the appropriate equipment).
