It seems the issue is with addons that parse the combat log. There supposedly are fixes available, but at present, if you're running a damage meter or other combat log parse, you should most likely turn off your out-of-date addons until they've been updated. I can attest that at present, Skada does not seem to work at all with 4.1, and I'd definitely recommend turning it off.
Updated: Check your favorite addon sites for updates to patch 4.1. While I can't promise your personal favorite addon will be up to date, Skada has released an update that makes it usable with the current patch as of 5:29 PM eastern.
WoW Patch 4.1 is live, and WoW Insider has all the latest news for you -- from guides of the revamped Zul'Aman and Zul'Gurub to new valor point mechanics and new archaeology items.