Not sure if they're "weird" references, but Blood makes a whole lot of references to the Evil Dead series, from one-liners to monster and item design. There's also a part of the game in which you can find a frozen Jack Torrance from The Shining.
The whole of the Guilty Gear series (two titles of which can be bought via GOG) is filled with metal, punk and generally rock references, ranging from subtle (Sol Badguy as a tribute to Freddie "Mr. Bad Guy" Mercury) to blatant (Axl Low/Axl Rose).
In Broken Sword II: The Smoking Mirror there's an easter egg that, if you meet all the requirements, lets you see Beneath a Steel Sky's Robert Foster/Overmann (both BaSS and the Broken Sword series being made by Revolution Software).
Most adventure games make references to each other, but a lot of them reference the Monkey Island series. Most of them have, quite literally, "red herrings" (as the workshop in Sanitarium with a large red herring painted on the roof, or the big crashed bus in Primordia, painted red and named "HerringBus").
In Silent Hill 3 there's a part in which, if you try to search a toilet, Heather Mason will say she doesn't know who, in their right minds, would do such a thing, in a clear reference to the previous game's protagonist, James Sunderland, who accepted every command the player gave him when it concerned searching through toilets and trash cans.
These are just some of the loads of examples I can think of... there are lots more, even in the games/series I mentioned.
Post edited July 28, 2013 by groze
