See http://business-news.thestreet.com/philly/story/9-great-collaborative-beers/11997284?page=2 for their list of 9 great collaborative beers. Best I've had was Gnomegang (Ommegang & Brasserie d' Achouffe)
Currently: I am a big fan of Urine Trouble. Surly/Three Floyds Collab. Not sure overall. I'd have to think on it.
I have had only one collaboration as yet. It was devils backbone and heavy seas for a black lager called Land Ho! It was my very first schwarzbier and I only wish I could have another so I could really see if my rating was good enough. I liked it. Not too many shwarzbiers at the store.
I had a St. Somewhere/Prarie sour saison down at Max's that was incredible as well as the De Proef/Sly Fox Broederlijke Liefde saison that was one of the best I've ever had, and I scored the bottle for about 5 bucks.
Collaboration Not Litigation. Take two of my all time favorite breweries who both Named their beer the same thing....then instead of getting into a pissing match you collaborate on a beer together! WIN
Love this beer as well! Also a vote for Fistcal Cliff - http://beeradvocate.com/beer/profile/22072/91716