It seems the most popular subject for MMD videos besides the Vocaloids themselves is Touhou; not that that's a bad thing.
I think this 20 minute long Reimu vs Cirno video is the best animated Touhou fight besides the Reimu vs Utsuho one.
I'm always anticipating the next MMD Cup; watching MMD videos has become something of a hobby/addiction of mine.
While this is not a MMD Cup video, it's one a pretty funny short video ; the use of Evangelion's OST is perfect: