Not sure if this was already posted by someone else but this is what I do after manually uploading Applications (.app) through SSH. I use a Mac, so I'm not sure if it works the same way on a PC:
1. Make sure iTunes is open and your phone is connected to your Mac
2. Upload however many apps you want
3. Off and on your phone
4. Your phone will hang at the boot logo for a long time and will vibrate twice 2-3 times, with quite a long break in between (at this time, your iTunes will be frozen with the colorful spinning wheel cursor)
5. WAIT... (maybe 6-10 min). After some time your iTunes will detect and display the iPhone page
6. Once iTunes shows the iPhone page, just reset your phone using the Home+Power button combination.
Your phone will reboot normally.
Kept restoring everytime it hung at the boot logo previously, until I decided to have some patience.