I have to believe this already exists but my search foo sucks so I threw together a small app/script to retag questions for helping me fix some bad tags.
For example you can search for tags with foo and bar then say remove bar and add moo. I have not automated it yet (not sure I will). It just gives the top 30 questions and has a button to manually apply one question at a time.
The script is not done but I can't test it unless I make this post according to the docs. Of course the docs don't make it clear at all what I'm supposed to put in this post. They just say I have to post it.