This morning Jay Freeman (@saurik) release Cydia 1.1. This update makes Cydia “faster, slimmer, and more stable; including an improved search algorithm and resume where you left off.”
When it was first released it was running a bit slow but now that the rush of people downloading it is over it’s running great.
Also, don’t worry about some of your sources being uninstalled during the process. They will still be there as explained in this tweet:
Here are some screenshots of the new Cydia.
UPDATE: While writing this article, version 1.1.1 was released. As of now, I do not know what changes where made but if we find out, we will let you know.