Eliza has vowed never to do full nudity. She wasn't in American Beauty. I believe the answer to this question is "No Movie". She has of course appeared scantily clad and partially nude in several flicks and in Allure magazine.
The Alphabet Killer (2008) - showing bare breasts while changing in locker room
The New Guy (2002) - modelling a variety of skimpy bikinis while dancing
Soul Survivors (2001) - kissing her girlfriend while massaging the girl's nude tits
Jay and Silent Bob Strike Back (2001) - drunk while pulling up her top halfway
Bring it On (2000) - in a skimpy bikini spraying herself with water at a carwash