Minecraft – How to have separate plugins for different worlds

Yes, this is doable, but you will need, as ratchet freak pointed out, a separate copy of minecraft for each set of mods. multiMC is one way to do that, but if you upgrade to the new launcher, you can create custom profiles, each with a separate set of mods, to make it even easier (see here for details, since the new launcher adds a couple of steps to the modding process).

Also, once the new launcher is more mature, and Mojang finally get around to providing official mod support, the whole process of switching mods on and off will probably get even easier.

I'm not sure that you understand what you are trying to attempt. If you set up a minecraft server using bukkit, then you will always be loading the same world, unless you manually change what world is going to be loaded in the configurations, and even if you did, it would still load the same plugins folder as it is in a set place.

Sure, you can copy and paste the whole bukkit+server+properties+plugins and use a different folder for different worlds+plugins+properties, which would allow you to have separate plugins, but for what you are asking, there really isn't a simple point and click method for separate worlds having separate plugins.

If you want it to load a different world with its own plugins, just make a shortcut to the bukkit initializations in each of the folders you create, so its easy to choose which to start.