Yes it's something I put a lot of thought into, that rare occurrences happen every game. It ups the 'oh crap' factor. Especially if you hit the player with it all at once. Like my last game you hit a star system having NO IDEA what's in it. Then BAM, space whales. Or you snuck through the system last time but this time you are decloaked and so now the pirates are coming at you.
Freakin' Game Hunter found Romulans and Space Whales in the same game. That was fun to see. He never did find a pirate system, they were too rare and depended on how many asteroids...it was complicated. ;-)
There were ion storm systems (messing up your cloak) and black holes (pull you toward the center each turn) but they didn't make the final cut...
To do this truly well you need to have quite a bit of content. If doing a linear dungeon dive (or tower climb or starbase jaunt or cavern rappel...) you might want to keep track of how many level's it has been since a Rare happened, and increase the likelyhood.
So on a roll of 6+ the level has a 'rare' event. +1 to the check for each level passed without a special. Rares can be special monsters, special rooms, puzzles, artifacts, hidden corridors, etc...If you are truly bad ass maybe the entire level is special.
And all this can change depending on what you are doing. I'm talking single screen linear dives here.