Tsukihime has stood the test of time best for me. Every time I boot it up, I realize once again why it's so amazing. Many VNs are just stock high school fantasies with a twist or two; Tsukihime is a work of art. The plot is dark and gripping, the descriptions and imagery are masterfully crafted. And Tohno Shiki is a wonderful character, probably my favorite from any VN, heroes and heroines. The combination of his fearsome eyes, frail body, and gentle heart give him a sense of depth appropriate to the plot and conflicts. He is one of the few VN heroes who doesn't just seem like a stock character thrown in as an afterthought while the game revolves around the girls and getting them naked/ecchi or to date you. He is a special and meaningful character, which I think adds a lot to the game.
In contrast, a VN like Snow Sakura is great to play through. It had its share of gripping storylines and admirable girls, but it's not a work of art like Tsukihime. The plot, while pretty good, still feels subservient to the girls and the eroge. The male hero is generic. The writing is much more mundane. Even the artwork, while slicker and technically more sound than Tsukihime, lacks character of its own.
Last night, I went through [Tsukihime] again. Clean install, no saves. And...somehow, it wasn't as awesome as my memories hyped it up to be. I was initially planning on Arcueid's route, like the first time through, but even she herself was not the appealing naive heroine I remembered. Rather, she's a cute but major pain in the ass ditz that throws scary as hell temper tantrums. This time, I found myself gravitating towards Ciel.
I never liked Acrueid much, Her route and character are the most generic and derivative. Personally, I thought the routes of Akiha, Hisui, and Kohaku(although, as is said, she is the "straw man") were where the VN's storytelling was at its best.