What if you omit the ModLoader.registerBlock call, will that hide the blocks from NEI?
I'm curious about this, because a couple mods I've ported did not register all of their blocks, presumably since they weren't meant to show in NEI (having corresponding items to use instead, same situation as yours). And they didn't. Is this why? Is this the reason why those mods did not register their blocks, or if not, is there any legitimate reason for a mod not to register all the blocks it uses? (because missing block registration can cause problems in Bukkit..)
calclavia, you may also want to look into the method to add items to the creative inventory - I've heard, but not confirmed, this is where NEI gets its items (along with any other items added by plugins). Notice how, for example, the vanilla Crop Block does not appear, since it only naturally exists in the world as a block not in player inventories as an item. But the water and lava blocks do appear, so I don't know. And Buildcraft's "pipe" block (default id 166) is completely hidden somehow, even appearing as available if you show all unused IDs, though it isn't (again, since it's created by placing corresponding items, not the block itself). If you do figure out the story here please post the details, since I want to know too