Those applications for which it is not a good idea to rename them have a built-in safeguard: they won't allow it. At least I've run into some that refuse. Perhaps it's a permissions issue that can be tweaked, however. But, I've changed names of some (just to include the X.n.n version number) and that hasn't caused a problem.
If you change the names of any Apple apps (built-in or not), you should be aware that it will cause updates to put the new version alongside the old instead of replacing it, and that your Dock icon will continue to launch the old version. Not that big of a deal, but you'll need to remember to check your changes after applying Software Updates .
NOTE: I believe this would also apply to 3rd party apps that update themselves from within the app. That includes anything using Sparkle, like Growl, Pixelmator, Adium, Handbrake, 1Password, Transmission, Colloquy, and many, many others.