Well I have a pair that have really made me think!!! Or at least notice them XD
Seinen has
Hotel by Boichi because it's about of what's to come one day in the future... It makes you actually think of your own future and the oen you'll leave for your kids...
Yaoi has
NightS by Yoneda Kou, because it's..... Deep... has a good dialogue with a remarkable speech.... Nice plot and a hot sex scene withot going all Hentai or stuff like that XD
Besides those I can only think of
1/6000 Honesty which is not as deep as you would expected yet is a regular read, the problem is that it's really long for a one shot (100+ pg!!!) and
Island too... But I prefer Hotel over Island actually
Signs,
Green