[lucas9000]

pokertracker pros:
-automatically import observed hand histories
-greater statistical detail (by far)
-more useful for analyzing your play and that of others

pokertracker cons:
-only works with hold em
-won't track live play, or play at sites that it doesn't support

pokercharts pros:
-can track live play, online play, and across any game
-web-based so you can access it anywhere
-pretty graphs

pokercharts cons:
-must manually enter sessions
-no real statistical detail about yourself or opponents other than results
-export function doesn't export all data (at least last time i used it)

if you primarily play hold em, pokertracker is the clear choice. but if you play a lot of live poker and/or games other than hold em, pokercharts can be good for accounting purposes at least.

fwiw, i'm going to shell out for a year's subscription to pokercharts, and already have pokertracker. because i play live and online, and various games, it's worth it to me, if for no other reason than for accounting.