There are lesser, basic, and greater mutagens. If a mutagen has no prefix, does that mean it's basic? And if every mutagen has its own "greater" version, does that mean its safe to sell every non "greater" mutagen if I want the best?

Not every mutagen has lesser/greater. There are a few (imo, useless ones) that don't. Like one that increases your sign range for instance.

That said, since mutagens drop like flies, and sell for quite a bit (especially considering their low weight), yes. Sell them, sell them, sell them. You're only going to use a few in your entire playthrough.

I just stacked all Greater Critical Effects, and sold anything else.

Thats what I always did, you have limited mutagens slots so there is no real point to use the 'lesser' mutagens. .

Take a look here: http://www.gog.com/en/forum/the_witcher_2/the_nearly_complete_mutagen_guide :)