There's only been a few instances that I can think of where these types of monster have been used properly or that don't annoy me.
1) Halo: Combat Evolved, the Flood: When they were first introduced it changed the pace of the game, you went from fighting smart enemies to trying to survive...and then they threw in fights where it would be you versus the Flood versus the Covenant. Three way battles where the enemies would attack each other as well. Hell you could even let them duke it out and mop up the survivors. The shit part of Halo 1 is The Library where you fight nothing but Flood in the same corridors over and over. After Halo 1 Bungie completely forgot about everything but the Library as that is what they kept doing, making you fight Flood and Flood only. Especially in Halo 2, and in Halo 3 they had the level "Cortana" which is possibly even worse than the Library!
2) Gears of War 2, the Sires. You spend 5 minutes of the level here and you have a chainsaw on your gun. Run, hold down B, have fun.
That's pretty much it! Every other game that has done has had all the fun sucked right out of it. Games are supposed to get better when you get towards the end, not cause copious amounts of boredom and rage! Personally I blame Bungie for doing it in the original Halo. Yes I bet it's been done before, but as with a lot of things from that game, when they did it very well and sold shit-tonnes, every other bugger on the planet had to do it as well. Thank fuck Halo: Reach contains no Flood what-so-ever, and is better for it. Seriously it may just be the best Halo game for this reason, well that and the Elites are back as enemies.