PotionEffect,StatList,Session,WeightedRandomChestContent,Explosion,ExtendedBlockStorage,SaveHandler.
All NBT patches seem to have been merged upstream, so removing. The IntegratedServer and MinecraftServer pending queue changes also removed, as fixed upstream.
Some notes:
Almost all int x, int y, int z parameters have been changed to BlockPos class
ForgeDirection has been removed, replaced by net.minecraft.util.EnumFacing.
All FML classes have moved from packet cpw.mods.fml to net.minecraftforge.fml
Fluid Rendering has been disabled for the time being, to be re-evaulated and a test mod created for it.
Minecraft now uses a Model based system for rendering blocks and Items. The intention is to expand the model format to better suit modder's needed once it is evaulated.
As such, The model loaders from Forge have been removed, to be replaced by expanding vanilla's model format.
Metadata has been extracted out in Minecraft to IBlockState, which holds a list of properties instead of magic number metadata. DO NOT listen to the fearmongering, you can do EVERYTHING with block states you could previously with metadata.
Stencil Bits are disabled entirely by for the main Display, Modders must enable and recreate the FrameBuffer if they wish to use Stencil Bits.
LexManos