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I almost always use AF. Exceptions would be and should be macro, astro, landscapes if you're using hyperfocal length focusing techniques, low light situations where the AF doesn't get enough light to work (a Speedlite can focus assist here), and if you're using a teleconvertor on a lens sometimes the AF won't work if the widest aperture is smaller than f/5.6.
If you're having trouble with the AF being off/inaccurate, check what AF points you're using. I nearly always just use a single point for whatever composition I'm shooting. I don't trust the multi-point one, because you don't know what you're going to get. Also check if you're in AI-servo etc focusing modes.
I was having trouble with my 40D front-focusing - I would point at something and the lens would AF, but the actual shot was focused in front of the objects. I sent the body away to get calibrated, cost $80, and it's spot on now. Couldn't be happier.
Lenses can also need calibration. Test all of your lenses, if your shots are consistently focusing the same (ie all in front or all behind), then maybe the body needs calibrating. If you only have one or 2 lenses "off", or some are focusing in front, some behind, then maybe it's the lenses that need calibrating?
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