1. Very small; this is the root of its use as a quantifier prefix.
2. A quantifier prefix, calling for multiplication by 10-6 (see quantifiers). Neither of these uses is peculiar to hackers, but hackers tend to fling them both around rather more freely than is countenanced in standard English. It is recorded, for example, that one CS professor used to characterize the standard length of his lectures as a microcentury — that is, about 52.6 minutes (see also attoparsec, nanoacre, and especially microfortnight).
3. Personal or human-scale — that is, capable of being maintained or comprehended or manipulated by one human being. This sense is generalized from microcomputer, and is esp. used in contrast with macro- (the corresponding Greek prefix meaning ‘large’).
4. Local as opposed to global (or macro-). Thus a hacker might say that buying a smaller car to reduce pollution only solves a microproblem; the macroproblem of getting to work might be better solved by using mass transit, moving to within walking distance, or (best of all) telecommuting.