Rise of the Triad had bonuses for various things, including the bonus bonus for getting all bonuses. Dunno if that counts, as the bonuses aren't permanent to a profile.
Not surprised that such a ground-breaking game as RoTT might have been the first to do it. That game gave me fits to finish. I still have it in my game archives. I honestly don't remember the bonuses that much but I do remember it was the first game to feature jump-pads; something that wasn't done again until 5 years later in Q3. That was when Apogee (3DRealms) knew how to make games.
Most visitors here probably have no idea about Rise of the Triads (1994). In a nutshell, it was originally to be the sequel to Wolfenstein 3D. But, Apogee (also known as 3DRealms - developer of the Duke Nukem series) who was the distributor for Wolfenstein 3D decided to take it in a different direction.
Some of the items that were used first in Rise of the Triad before any other game were:
* Parental Lock of objectionable content
* Random game enemies (the same enemy wouldn't always be in the same spot when you replayed the game)
* Non linear episode progression (ending one specific level wouldn't always take you to the next one)
* Jump pads
* Bullet holes in walls
* Ability to jump on top of objects in a game
* Live Remote Ridicule (insult people in a LAN game using a microphone - forget those built in insults!)
* Enemies that play dead instead of just dying immediately.
* Rocket jumping
* Capture the Flag
http://www.3drealms.com/news/rise_of_the_triad/