I'm pretty sure a lot less than 99% of full screen movies are straight pan & scan. I bet at least 25% of all widescreen movies are matted in some way. Kubrick is probably best known for doing this with his later films. I'm just thinking off the top of my head. The new disney dvd's for The Jungle Book Robin Hood and Aristocats are all cropped to widescreen. (And I don't think there would be any boom mikes to worry about in animation.) One of the Pirates of the Carribean movies (all Super 35) was misframed in the widescreen version. I'm pretty sure The Pursuit of Happyness is another super 35. I saw it at an advance screening and it looked like a 1.85:1 movie. I was surprised to see the widescreen dvd 2.40:1. They say a matted widescreen is correct because that's the way you saw it in the theatre but that wasn't true in my case. A dvd preview on the Casino Royale dvd is 1.85 and it shows more on the top and bottom.
Here's some examples for the Harry Potter films. (Anybody know how Order of the Phoenix was shot?)
http://plum.cream.org/HP/
Anybody know whether these films are open matte?
The Ten Commandments
Animal House
Airplane
Sixteen Candles
The Breakfast Club
Top Gun (one of the few older movies to get a special edition rerelease with a seperate full screen version from Paramount)
Pretty In Pink
Some Kind of Wonderful
What's Eating Gilbert Grape?
The Naked Gun (all 3)
Home Alone
Better off Dead
Robin Hood: Men in Tights
The Truman Show (The new dvd shows slightly less on the top and bottom the Trutalk montage with the mock LIFE cover is a good example)
A Beautiful Mind
Lost and Delirious (Lea Pool- 2001)
Stardust (Great movie! go rent/buy it. It's 2.35:1 and a user post on IMDB said it was hard matte. Still I'm sure I saw more on the top and bottom in the theatre than some of the widescreen clips I've seen online. The theatre screen looked about 2.15:1)

What I wish is that studios would give a full screen dvd release only for open matte films. For example Scorsese shot many of his films like Goodfellas in the 80's and early 90's so that they could be also formatted for 4x3 tv. He has returned to true widescreen with more recent films like The Departed. Guess which movie Warner made available in full screen?
And I know that it costs more to do a pan & scan transfer. Is that also true for making an unmatted release?