Backup and restore application preferences I already have a backup of my system on Time Machine, but will it restore my application preferences too when I migrate to a new system? Even if it is Lion? (I come from Snow Leopard) 
And what about those apps that have their data in Library>Application Support?

Do I have to manually copy and restore .plist files or is there a Backup app smart enough to copy them together with the .app file?
Your preferences will be copied if you allow Migration Assistant to copy your data from a Time Machine backup (one of the options at the beginning of the installation).

Time Machine backs up just about everything except Mac OS X and other system resource files. So, your preferences will be saved.

I've tested this migrating from 10.6 to 10.6, and I've migrated from another Mac directly from 10.6 to 10.7. That process is, in practice, the same.
So, your preferences will be copied from your Time Machine backup to your new system.