Although
Poker Tracker was the first tracking program and probably the most popular in terms of # of users, my personal preference is
Poker Office, but to be honest I only use it for the "heads Up" display, that shows the opponents mucked cards instead of constantly having to go back and look at the hand histories.
There is an increbilbe amount of information that can be gathered and used for game selection and tracking of players. If used correctly it can give you a big edge. I'll try to find a good tutorial for the program and post a link.
Jason