In our 25M raids as of just recently, we've started seeing people experience serious frame lag (as in makes the game basically unplayable) around the same time as stampede is used on certain fights, most notably Sha of Fear and Amber Shaper Un'sok. I still can't conclusively say that it definitively is stampede, as eliminating all other variables would be ridiculously time consuming and not really reasonable during limited raid time when we are trying to get things done. But it does seem to correlate pretty well with when we do use it, and when we stopped used it.
Basically I was just wondering if anyone else has experienced this. I posted about it in the WoW bug report forums and also bumped a thread mentioning similar issues in that same forum, but they seemed basically ignored.