I've seen a lot of people call CraftBukkit a server mod. I found some other SMP mods I would like to install but they only have instructions for the basic minecraft_server.jar. Is it possible to add other SMP mods to CraftBukkit or have them running in conjunction? I've looked around a lot, but haven't found anything. I may be using the wrong search terms, most of what I found ended up linking back to bukkit and how to install it. Any help is much appreciated, thanks.
Most of the time, what you're looking for are plugins. If someone has a mod that doesn't work specifically with CraftBukkit you're most likely out of luck.
Yeah, most mods that modify the internal classes of the server aren't going to be compatible with Craftbukkit, but you can always talk to the mod developer and ask them if they could try to code a bukkit plugin for it.