Because I can imagine (a limited number of) situations where a version tag is useful, I propose we follow the suggestion Rarst gave and create [version-*] tags, and only use them when really needed. Everyone (with 150/500 rep) can help clean up by subscribing to the wildcarded [version-*] tag, and retag when a question is not really tied up to a version. I think we will have fewer mistagged [version-*] than mistagged [wordpress-*] questions, so keeping it under control should be easy.
I'm going to question the value of this tag. I think we should remove them all since most questions are about v3 and most questions are not tagged with [wordpress-3] or whatever. I think if a tag is likely to apply to more than 25% of questions it starts to be not applicable, especially since many people won't tag their questions as such and there is a limit to the number of tags that can be used.
Tags should be for specifics, not for generalities. At least IMO.