I am currently on iOS 4.0, unlocked and jailbroken. If i upgrade to iOS 4.1 (locking the phone again), when the new jailbreak/unlock comes out will i be able to recover those paid cydia and rock apps?
Yes you can. Either you can rely on Cydia to remember all of the apps that you purchased, sometimes it works, other times it doesn't, or you can prepare before you update and download PkgBackup which will assist you in restoring your JB apps.