Godfather is definitely one of those films for me as well. I used to just hate Coppola in general, but I have actually gone back and fallen in love with Apocalypse Now. And I've tried the same with Godfather a few times and I still just don't get it. Even with all its flaws, I think Once Upon A Time in America is significantly better. Goodfellas, for me the high-water mark for the gangster genre.
Dante Tomaselli's films - I don't know how well their reputation has held up, but I remember when "Horror" came out, he was held up as the next big thing. And, I just never got that. Even gave Desecration and Satan's Playground a shot, but he still seems amateur and silly.
Exorcist - I can get its place in history and the significance that it holds as one of the first blockbusters of horror. But, I have always been surprised that this gets held up as one of the greatest horror films of all times. I think it has some great shocking imagery, but as a film, I find it rather sloppy and uninvolving.
Star Wars - even as an 8 year old kid during the whole phenomenon, I never understood why this was such a big deal. Sure, lightsabers were cool. But that was really all that I dug. I did love Empire Strikes Back though.
Most Comedies - in general, I guess I am very discriminating about humor. But, most comedies, particularly in the past 20 years, normally leave me feeling rather "blah" Even the comedians that I really like, such as Ben Stiller, Steve Carrell, and Tina Fey, rarely make movies that I enjoy as more than disposable time wasters.