iPhone 3GS stuck on home screen after updating Cydia
Try booting into Safe Mode. Safe Mode disables all tweaks, and unless the tweaks use something else, will not start Mobile Substrate.

Force shutdown your phone. Now, turn it on. Hold down the volume up button until the phone turns on. 

Now you are in Safe Mode. Delete all tweaks, and slowly install them back, one by one, so you can see which one is causing trouble.