Midday Moon (Hisui's True Ending) and DREAMS OF SUNSHINE[footnote]Yes, it's actually written in all caps like that, to distinguish it from Dreams of Sunshine (Hisui's Good Ending).[/footnote] (Kohaku's True Ending) from <url=http://www.escapistmagazine.com/forums/read/326.128851-TYPE-MOON-reviews-Tsukihime>Tsukihime were phenomenal. The former stood out among all the game's endings as a true "holy shit" moment of dawning realization and incredible bittersweetness, and I can't describe the latter without spoiling it.
Mizuki's endings in <url=http://www.escapistmagazine.com/forums/read/326.135672-Neutral-Drow-reviews-A-Drug-That-Makes-You-Dream>A Drug That Makes You Dream made her route stand out even compared to Aeka's entire route (which was the best overall). Mizuki's unhappy ending was almost out-of-the-blue, but then you realize that it makes some sense...which just twists the knife of tragedy more. If her happy ending hadn't been almost indescribably heartwarming, I probably would have been crying for days in sadness (as opposed to just two days, in happiness).
In fact, <color=white>Makoto's ending in <url=http://www.escapistmagazine.com/forums/read/326.163769-Neutral-Drow-reviews-Kanon>Kanon was probably a good indicator of what would have happened if Mizuki only had one ending. That route actually invoked something uncomfortably close to genuine grief.
And finally, for a less positive effect...Silent Siren (Hina's Sex Ending) from <url=http://www.escapistmagazine.com/forums/read/326.148564>Little My Maid. One of the most infuriating things I've ever read. Not bad, per se, it just evoked quite a feeling of guilt, horror, and rage that I found somewhat uncomfortable.