I currently have accounts with both Mint and Wesabe. Both have limitations, but of the two I prefer Mint. I'm keeping Wesabe because I have a year of transaction classified there. I can export those, but Mint can't import them! One of its limitations. Also, Wesabe promises (and promises) to improve.
For evaluating any of these I recommend checking the forums. See what the current hot gripes and wish list items are. Are those things you care about? See what the communities are like. Are they anywhere near as friendly and knowledgeable as DonationCoders, for example.
+ Able to enter manual transactions
- Horribly slow, painful user interface. It helps if you start with a fresh browser session and restart when things get slow. Seems like they are doing something that exercises Firefox's memory leak. They've taken lots of heat on the user interface and say that they have improvements in the works, but I haven't seen the things I've been looking for.
+ Highly capable of connecting to all my financial institutions. Easy, quick set up.
+ Much more intuitive, faster user interface.
+ Better at automatically classifying transactions.
-- Can't enter manual transactions.
? Recently acquired by Quicken. Google "mint quicken".
I've barely scratched their abilities to present graphs, do budgets, make recommendations, etc. I can't stand accounting activities, so I'm looking for something stone simple that will do as much of the work as possible automatically. Nothing is quite there yet.
Good luck. --David