Peeron also does that. The website can be a little slow, which can be annoying when you have to add lots of sets.
Brickstore is made for managing a Bricklink store, and because you sell either sets or pieces there, you add either the sets or the pieces in a set. You could of course create two files: one listing all the sets and another listing all pieces. That's why I only use it for bulk bricks. Peeron has the advantage that you can add sets and still check how many of a piece you have, but as I said: it can be slooooow from time to time.