Boot to single user mode (Command-S) and see what fsck shows.
/sbin/fsck -fy- repeat the prior up to three times if needed
Assuming it boots, you can halt and then boot in verbose mode (Command-V) to restore all the console glory.
You can also peek at /private/var/log/system.log while on single user mode to see what was happening when the clock was passing faster than the gray progress bar.
I'm inclined to think something has corrupted your preference files or application data, as those will be brought back after a restore from backup.
In order to test this theory, you will need to wipe the phone by putting it in DFU mode, then restoring to the latest Apple firmware through iTunes. Then set up your device as a new device. If the problems still occur (unlikely), then I would take it in to an Apple Store and have a Genius look at it.
If, however, it fixes the issue, then you will have to play "hunt and go seek" with the culprit. Restore your backup, jailbreak (but don't install anything from Cydia except OpenSSH so you can access the file system), and root through your "home" folder (/private/var/mobile).
You should try deleting the preferences (plists) first (~/Library/Preferences), then rebooting. Don't worry, iOS will recreate them. If that doesn't fix it, try removing the sqlite database in ~/Library/Twitter, although I have a feeling the preference files should take care of it.
I wish I had an easy answer for you, but it's going to take some study of the file system and tracing back to the package that "infected" your system.
Not everything in Cydia is deemed safe and you may wish to exercise more caution in the future. MobileSubstrate (which is only made possible be reverse engineering) provides the hooks for many deep level APIs that shouldn't be messed with.
Additionally, you may want to hit up jailbreakqa for additional help, as that is the official forum for help on these matters. From my experience, there isn't much help here regarding this process.
Best Answer
If you mean MobileSubstrate SafeMode…
Since it has happened multiple times, restarting hasn't seemed to fix it. Consequently, I would recommend performing the following:
Remove recently installed extensions.
If you know that you recently installed a Cydia package, or updated one, I would suggest uninstalling that package and see if it makes a difference.
Use Crash Reporter.
Crash Reporter will attempt to guess the cause of a crash. After installing, next time your iPhone crashes, you can check the 'Possible Causes' list in Crash Reporter for its guess on the cause. You can then try to delete the package in Cydia and see if that fixes the problem.