The most complete mileage manager and the one that's been in business the longest and which doesn't have a thread for problems (ala the thread for miletracker) is the original: MileageManager.

mileagemanager.com

As it is Web-based, it tends to be available wherever you are, at home, at the office or even on vacation and no worry about hard-drive crashes, operating system incompatibility and even more important these days, viruses on your machine.

Anyway, hope this helps.

P.S. and MileageManager helps fund making FlyerTalk available to all.