Look at it this way...
---If you take a Jailbroken Phone to the store, they won't fix it.
---If you take an unjailbroken phone to the store, they will fix it.
If you JB'd your phone and it goes screwy, do a RESTORE to the official Apple iOS version (a basic 5.0.1 or whatever iOS version you were on) and you got your warranty back and you'll be able to get Apple to fix it for you.
Don't expect them to fix your phone if they see Cydia or any other JB apps on it though.