If you upgrade iOS with iTunes, your device will be un-jailbroken and Cydia packages will be deleted. Before upgrading iOS, make sure a jailbreak is available for the new version.
Untethered jailbreak for iOS 6.x
As of March 19, 2013
If your device currently has a tethered jailbreak on iOS 6.0, 6.0.1, 6.1, or 6.1.2: you can install the package evasi0n 6.0-6.1.2 Untether to untether it.
If your device is not jailbroken on iOS 6.0, 6.0.1, 6.0.2, 6.1, 6.1.1, or 6.1.2: You can use evasi0n to jailbreak it untethered.
If you want to upgrade your device from an earlier iOS version:
Apple has released iOS 6.1.3, which means that any attempt to downgrade/upgrade/restore to an earlier iOS version with iTunes will fail with an error message. You cannot downgrade/upgrade/restore to earlier iOS versions using SHSH blobs on newer devices. Older devices that can use 6.x SHSH blobs are iPhone 4, iPhone 3GS, and iPod touch 4th gen.
How do I find my current version?
Open the Settings app, tap General, tap About, and look at Version.
(Your device's version is also listed at the bottom of the Cydia "homepage".)