Installer.app, the app store before that other app store, is coming back for firmware 2.0 and being re-fashioned as Installer 4. Currently, jailbroken 2.0 iPhones are using Cydia as their main app pipeline but when Installer 4 is released, well, they'll likely play nice with one another and especially nice with that other app store.
The RiP Dev Blog has a lot of complicated, programmer's type language describing the updates for Installer 4.0 so I'll try to translate to more understandable, layman's terms: It's going to be faster, safer, and more integrated. Bang.
The release of Installer 4.0 seems to be imminent but well, really, there's no rush, many of the apps that were available for 1.1.x aren't quite ready for the big time yet. So take your time with Installer 4.0. We here at TiPb would almost always prefer a little delayed polished product over a rushed, rough, not as advertised..yeah, we're looking at you MobileMe.