I've got a couple. They may not be quite so simple, but I've got to start somewhere.
1) Could a crash/specific mods somehow screw up mob spawning so that they no longer spawn in any noticeable quantity? At some point recently in Horizons SSP, monsters just don't spawn at night, and the Nether is quiet and boring. More importantly, is there way to fix/edit this?
2) How many mods does Biomes O' Plenty render infeasible? I can't find any fun GasCraft blocks and it's been proving difficult to find some Ars Magica 2 things as well. I suspect BoP biomes might also be hampering spawns of things like AM2's Dryad and Thermal Expansion's Blizz... which sucks, because I'd either have to try and find a vanilla biome somewhere and hope it will actually spawn Blizz/Dryads with the aforementioned spawning issues, or reset and lose several days of building and spellcasting.