Since you have full access to the iPhone file system, it is very important that you know exactly what you are doing, and what you are installing from Cydia.
Cydia is great and there are lots of resources that prevent you from accidentally installing the wrong iPhone hack or application. For example, some iPhone hacks in Cydia will not install simply because you don't have the correct iPhone software or iOS firmware version number.
It is very important to know that you you install things from Cydia at your own risk and Apple will not help you at all.
Before you install any Cydia App or hack you should start by carefully reading the iPhone hack description. It will tell you what the hack will exactly do, and if it is compatible with the iOS you have installed on your iPhone or iPhone 4.
iPhone Troubleshooting usually is straight forward and simple with a non-jailbroken iPhone. A restore from iTunes will most probably solve any of those problems you might have. However, with Cydia Apps installed, the iPhone problems will be a little different, and restoring you jailbroken iPhone is not the best solution as you will lose your jailbreak.
The Level of the Problem:
Every now and then I run into some minor iPhone problems with a Cydia application or an iPhone hack. Most of the times I can solve those problems right away by a simple iPhone troubleshooting, but sometimes it take more time and effort to figure out.
Safe mode is a nice protection feature of the Mobile Substrate that allows you to start your iPhone with all extensions, plug-ins, iPhone hacks, and Cydia apps temporarily turned off. It gives you the chance to run Cydia and remove or uninstall the Cydia app the might be causing the iPhone conflict.
Safe mode will start automatically when the iPhone senses a conflict, and when the lock screen can't start. However, you can manually start safe mode from SBSetting if you want to disable your installed iPhone hacks for any reason. Open the SBSettings menu, and then tap the Power button. Then tap Safe Mode. You iPhone will start in Safe Mode.
Those iPhone problems that happen immediately after installing a hack from Cydia causes the iPhone to start in Safe Mode. Once you get this safe mode screen, you should know immediately that the last iPhone hack that you just installed has some compatibility issues, and that you should uninstall it immediately.
Simply open Cydia from the home screen and uninstall that last hack. Then, your problem should disappear.
Complicated Cydia Apps Problems:
Some iPhone issues happen over time because of a conflict between two iPhone hacks that doesn't happen right away and that doesn't cause major iPhone problems. The iPhone would function normally with some glitches in some iPhone features.
Those issues can happen when you run a specific Cydia application or hack, and notice that another iPhone hack or iPhone application stops running or functioning over a period of time. Therefore, it is very difficult to know which iPhone hack that caused the iPhone problem.
The solution to those types of iPhone problems could be very difficult to find, and it could be time consuming.
There are two ways to determine the root cause of such tricky iPhone problem. You can use the method of elimination by uninstalling one iPhone hack at a time from Cydia, and see if the problem will disappears.
Once the problem disappears then you will know the troubled iPhone hack and remove it. Then, you can send the developer a quick email about the problem to fix it.
I have had much success with Cydia developers fixing problems with many Cydia Apps.
Most of the times it is not that easy to diagnose and troubleshoot iPhone problems caused by a Cydia hack specially that you will be on your own solving those problems.
It is very unlikely that you can find someone who is running the exact combinations of iPhone hacks at the same time on the same iPhone or iPhone 4.
In that case, your best bet is to either restore you iPhone and then re-jailbreak, or wait for a new major iOS update and live with the problem until the next jailbreak.
The most reliable solution is to remove the Mobile Substrate all together which will uninstall all the Cydia applications and all the iPhone hacks that you installed on your iPhone or iPhone 4. It will not remove Cydia of course, and you will not lose your current jailbreak.
Removing the Mobile Substrate will give you a chance to install all your Cydia hacks from scratch.
You can start re-installing Cydia apps one by one, and see if you get the iPhone problem you were getting. Monitor your iPhone performance after each iPhone hack until you see the problem happening again. Then, you you have found the root cause of the problem. It is a good idea after that to contact the author of the iPhone hack and report the problem to him so he can fix it.