When you jail break your iphone for the second time does all your previous apps and tweaks get removed?

LIke I've jailbroken my iPhone with the 3.0 firmware and now im waiting to jailbreak it with the 3.1. I've done a lot of cool stuff with my backgrounds and stuff through SSH and all my apps I've downloaded through Cydia. Will those stay on my iphone when I jailbreak it with the 3.1 firmware? Or will everything get erased and have to start over. Sorry if this seems like a stupid question but I just haven't heard anything about this before.