If you're not the type to stick around while Cydia updates, then we have a solution for you. A few new additions have appeared recently in Cydia that will allow you to update the cache that Cydia uses without actually running the app.
There are a couple of apps that perform this duty, and both of them run as SBSettings toggles. This makes it pretty easy to update Cydia while you check your email and then quickly load up Cydia to get your updates and new packages.