Why is my jailbroken iPhone not booting?
Solution 1:
I've had this happen once before. Is your phone in an "endless loop" of reboots? If so, my solution was to put the phone in DFU mode and restore it and just try the jailbreak over again. Sometimes things get loopy and it just doesn't work correctly. Give it another shot.
How to Put an iPhone Into DFU Mode
Solution 2:
I had a similar issue with my 3G and was never able to get out of recovery mode, even with DFU mode. Luckily since I used blackra1n I still had the stock apple splash screen, and I was able to take it into the Apple Store where they exchanged it for a new one no questions asked. If you still don't have any luck getting it out of recovery mode, the Apple Store is definitely worth a shot.
Solution 3:
Try restoring using iOS4, and jailbreaking that using Jailbreak Me.
If you do not have the SHSH blob on file with Cydia, you will be unable to restore to 3.1.3 though I am unsure what the failure condition for that is.