The same thing happened to me. I updated my previously jb i4 to 4.2.1, re-jailbroke and a lot of apps seemed to disappear. I ended up restoring and re-re-jailbreaking. Unfortunately, it took a couple of times doing that to work because I kept getting errors. I would love to know why this happened.
I have had another go at restoring the iPhone 4 and re jailbreak it after the whole restore and sync was completed and now it seems to be working fully with no apps missing
On another note, is there a way to list apps not supported by greenpois0n rc5 / latest cydia update? Tried qTweeter and installed it first time I jailbroke on RC5 and froze and couldnt use iphone until I restored it.