I don't remember if before I recently updated to OS 5.xx they used to work or not, but now whenever I plug in my apple in-ear headphones, the sound just comes out of the phone's speakers like nothing happened, what gives?

The 3.5 mm stereo ( no mike) should work but I would suspect the jack is causing the BB to think nothing is plugged in. The wire configuration on a standard BB headphone includes a microphone. I would try different ear buds. Ipod is a 3 wire and a BB is 4 wire.