Only Cydia is even available on 2.0, and there are no apps available to run on 2.0, because nobody has ported over their apps to 2.0 yet. However, since 2.0 is now officially available for everyone to jailbreak, we'll start to see our favorite jailbreak apps slowly be ported to 2.0. Installer 4.0 is one of those.
However, one thing you CAN do is install OpenSSH, where you can now get access to your file system and make any customizations that you want... I hear that App Store apps are stored in /private/var/mobile/Applications directory. Quite interesting!
I'm quite excited for apps that will run in the background. Take that, Apple!