Aloha yalag,
I noticed that you mentioned Cydia - that means you have jailbroken your iPhone, but that really shouldn't matter (other than some people who probably attribute any issues on a jailbroken iPhone to the fact that it's jailbroken

). I've experienced the same issue as yourself, on a non-jailbroken iPhone 3G, and it's literally driving me up the wall.
Here's a follow-on question. What about your non-Apple apps (to include the Apple Remote app)? Once this happens on my iPhone, none of them run - they ALL crash. When I hook up my iPhone to a computer and check iTunes, all of the iPod and iPhoto content is there, on the iPhone, but for whatever reason the iPhone is unable to display it. When I last took my iPhone to the Genius Bar at my local Apple Store, they told me that an .xml file, resident on the iPhone, is corrupt, but offered no way to troubleshoot the issue.
To make matters worse, at least for me, they actually insinuated that I was doing something wrong when I synced my iPhone with my Mac! It's not rocket science - we sync the iPhone 3G exactly like we did the 1st gen iPhone. I'm now on my 3rd iPhone and the same issue just cropped up again.
This issue is really driving me insane. I picked up my new iPhone, took it home, set it up as a new phone, then synced my music, video, photos, ringtones, and applications (I set up MobileMe syncing for my contacts, calendars, and bookmarks). Everything was fine last night, but this morning, immediately after I applied the 2.0.1 firmware update, this same issue reared its rather disgustingly ugly head yet again! All of my iPod and iPhoto content was not listed, and all of my non-Apple apps crashed. I, personally, think it's somehow related to the 2.0.1 firmware, but I'm not sure.
At this point, I have no solution to offer you - only my sympathy, as I'm going through the same situation as yourself. I'll most certainly pass on any information I get from my local Apple Store. I'm at the point where I'm going to just take my MacBook Pro, my external drive (on which I host my iTunes library), and my iPhone into the Apple Store so that they can assist me in the troubleshooting process.

HawaiiMacAddict