Funny how many Quake mods become games of their own. Then again, doesn't a fucking ton of games run on some sort of Quake engine (I know unreal is popular, but isn't Quake right behind it?).
Not for newer games. Unreal is definitely on top, the Source engine is undoubtedly in second, with id Tech being behind it. I don't believe Source shares much, if anything, with the Quake-derived GoldSrc engine. Even if it did, the current id Tech engines are a radical departure from the previous ones.
If you're including older games, the id Tech engines definitely beat Source. Technically, everything from Doom to Rage are consider id Tech engines (Doom being 1, Quake/Quake2 being 2, Q3A being 3, Doom 3 being 4, and Rage being 5), so that's quite a bit of market share over a good stretch of time.
Also so far I'm enjoying Metroid Other M. Seems fairly linear, but it looks like I'll have a LOT of backtracking to do (it shows items on the map, which is retarded IMO, but it's still fairly unclear how to reach most of them). The last boss I fought (This giant bee hive) was fairly goddamn hectic.
Most of the Metroid games that have in-game maps tell you whether there is an item in the room, actually. As you've surmised, the trick is actually finding how to get to them.
One perfect example is in Zero Mission. Near the end of the game there is a hidden item that is only accessible if you use a complex series of speed boosts and shinesparks (Samus's dash and mid-air charge moves, respectively) spanning about four or five screens to reach it.
Zero Mission also has a decently well-hidden secret in Brinstar. After you defeat Mother Brain, you can go down to see her lair in ruins. In the screen past her lair, there is a wall that must be dashed through (or rubble, I don't remember which). The only problem is that there is no room to do so. What you have to do is go a few rooms to the right, speed boost, then screw attack all the way through Mother Brain's chambers -- being careful not to hit the ceiling or land -- and blow through the wall and into the escape tunnel, then through the left wall and into a secret chamber. Basically, you have to put all of the pieces together and do a speed boosted screw attack.
So, yeah, finding the items has never been a problem. Getting them is the real puzzle. It's kind of a nifty take on the carrot-and-the-stick approach, and I think it suits the game well.