Nights of Azure is definitely up there, as that presents a believable, subtly handled romance between the two heroines that isn't the main point of the game, but supports its overall atmosphere.
The visual novel Ne no Kami that I covered last year is also a nice example of something similar. It's a yuri visual novel where the romantic aspect again isn't necessarily the main point, it's just another piece of the whole picture.
Plus I've gotta mention Grisaia. The relationships in that game are varied, fascinating and incredibly compelling to witness. The series will always be the benchmark for me on how to integrate sexual content with narrative, too.