Can I have different Minecraft mods in different worlds?

Is it possible for me to have different Minecraft worlds with different mods?

For example, say I have one world with Pixelmon and a few other mods (improved furnaces, craftguide and timber), and I would like another world with say, FTB mod, but not Pixelmon.

Is this possible?

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.