And with all this extra code...
As always, even with iPhones, iPod touches, and iPads, extra code means crashing and Cydia Substrate can solve this too. Should the SpringBoard crash for any reason (which is quite common once let loose on Cydia as there are a large number of SpringBoard extensions) Cydia Substrate will temporarily put the SpringBoard into Safe Mode with SpringBoard extensions disabled, so you can troubleshoot the problem.
If one is trying to troubleshoot a problem that isn't causing Springboard crashes but is suspected of being caused by a Cydia Substrate-using extension, Safe Mode can manually be entered using the SBSettings application available in Cydia by hitting its "Power" button and choosing the "Safe Mode" option.
If you find that your device won't boot, you can force Cydia Substrate to not run by holding down the volume up key while the Apple boot logo is visible. This requires version 0.9.3997 or newer. Devices without a capable version can be forced into Safe Mode from a ramdisk or ssh by typing: