...Negima X Monster Girl Quest. For some reason, having just finished Gabriel Blessing's Shirou Emiya: Erogame Protagonist, that is the first crossover idea that came to mind. It probably has something to do with the number of girls in both series, and I use that term relatively loosely.
I have couple rough, rough ideas as to how he'd end up in the MGQ world... but other than that nothing, though I feel like bringing Eva along with him would lead to even more shenanigans.
...or maybe fuse the two, and have the Negima girls (the human ones) be various monsters he encounters. Hmm... that idea deserves pondering.