Have you already tried the volume up button method to disable Mobile Substrate? You should also be able to connect to it over USB. See this guide to working with devices that won't boot:
Maybe you installed a very incompatible tweak? Try Mobile Substrate's safety feature: If that doesn't help, it could be that a tweak you installed before rebooting (even days before rebooting) is very incompatible with your version of iOS, which could cause a "boot loop" (getting the Apple logo over and over). Try forcing a reboot and then immediately holding down the Volume Up button as the device boots up. This will temporarily disable all extensions, as explained in the Mobile Substrate description.
Try manually removing very incompatible tweaks: If that doesn't help, or if your device is using an old version of Mobile Substrate (a version without the safety feature), try plugging your device into your computer and using an application such as iExplorer, DiskAid, or Phone Disk to access the device - it may be difficult to access a device in this state, but force a reboot and try accessing it. Check in the folder
/Library/MobileSubstrate/DynamicLibraries/ and delete any extensions that might not be properly compatible with iOS 5, and then try booting again. (If any of your extensions happen to be pirated, those are good candidates for removal because pirated software is often outdated and buggy.) Try this until it works, or until you run out of patience. :)
15 Jun '12, 19:48