I've been at the Genius Bar next to someone who brought in a jailbroken iPod Touch and the tech support guy asked him if it was, he said yes, and just gave him another iPod Touch. So take your chances.
---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.