No matter how many times I watch it, Samurai X always ALWAYS gets me, both Trust and Betrayal and Reflection... I also cried with the way they ended the Berserk anime.
Manga: Good Ending(Cried), Suzuka(Cried happily), 5 centimeters per second (not really cried but felt super sad)
Anime: Ano Hi Mita Hana no Namae o Bokutachi wa Mada Shiranai(Cried), Angel Beats (Cried), Onegai Sensei (Cried), Shuffle (Cried because [SPOILER] Kaede wasnt chosen), Clannad After Story (Cried)
The most popular name in this thread is Clannad. I haven't watched the anime but of the 3 routes of the VN I've done (Nagisa, Kyou, Misae), I've cried in all of them.
Air TV
Angel Beats!
Clannad
Code Geass
Crescent Love
Elfen Lied
H2o: Footprints in the Sand
School Days - Manly Tears were not shed for Mikoto
True Tears
There were a few others but it seems I forgot to mark them on my list of Anime.