Note: This isn't for people who are uncomfortable with command line. You need to perform this as root.
Normally you edit /private/var/stash/Applications/<appname>/Info.plist
You still need to edit that to what you want it to say, however.
You also need to go into /private/var/stash/Applications/<appname>/English.lproj/InfoPlist.strings
It's kind of a garbled file, but for instance, if you're trying to change the name of Safari, you would go into that file and delete the instance that says Safari (not MobileSafari, just plain Safari). Do not edit this, just remove it and the name you put in the normal Info.plist will be the new name of the app. If you use a language other than English, simply go into that folder instead of English.lproj
Normally you edit /private/var/stash/Applications/<appname>/Info.plist
You still need to edit that to what you want it to say, however.
You also need to go into /private/var/stash/Applications/<appname>/English.lproj/InfoPlist.strings
It's kind of a garbled file, but for instance, if you're trying to change the name of Safari, you would go into that file and delete the instance that says Safari (not MobileSafari, just plain Safari). Do not edit this, just remove it and the name you put in the normal Info.plist will be the new name of the app. If you use a language other than English, simply go into that folder instead of English.lproj