Hmm not really, probably the one I've gone back to play the most is Tsukihime. Recently played the Muv Luv series and while I enjoyed it I do tend to overanalyse and think to myself "that's ridiculous, why would that happen" or "that's silly, why would he/she do/say that?"
I don't have any manga/anime interest whatsoever so I sometimes find some of the plots and story archs to be so unrealistic that I have to slap myself and tell me its just a fantasy world scenario.