New features:

The transfer queue is now stored in an SQLite database. This greatly improves performance and vastly reduces memory consumption while loading/saving the queue
Additional improvements to general queue performance and memory consumption
The provided Linux binaries are now compiled for Debian Squeeze instead of Lenny
Bugfixes and minor changes:

Fixed crash during shutdown of FileZilla
Clearing the queue when it was not yet fully populated no longer causes a crash
If using ask login type for a site and no username is given, the initial focus is now on the user box in the login dialog