Noticed a major drop in FPS (from ~40 FPS down to 10-20 FPS) after upgrading from Minecraft 1.5 to 1.6, and believe I may have isolated the problem to the newer version of lwjgl bundled with 1.6. I get the exact same drop in FPS if I run Minecraft 1.5 and replace the bundled version of lwjgl (2.4.2) with 2.9.0, so I don't think this is due to any changes in MC 1.6, just to the newer lwjgl it ships with.
-I only have 1 GPU (the NVIDIA GeForce 8600M GT GPU), so this is definitely not a duplicate of the many bug reports involving MC 1.6 using the wrong GPU.
-Can replicate this in OS X as well as Linux, so I don't think it's anything in my OS environment.
-Changing the lighting settings (doesn't matter to what) gives a temporary speed increase back up to 40 FPS, but it always goes back down to 10-20 FPS after a few minutes.
Please let me know if there's any other information I can provide.