Maverick-shipping: Sigma (from Mega Man X) and Ryoko Asakura (from the Melancholy of Haruhi Suzumiya)
This may seem a bit weird, but to me it seems like a good pairing because Sigma and Ryoko think similarly. Sigma destroyed Abel City to have X realize his "potential", while Ryoko was willing to kill Kyon to have Haruhi produce "data" for her to collect. Doing this, Sigma went Maverick, while Ryoko's actions would be considered a "Maverick" act in the Mega Man X universe. If they were together, they could help each other's extremist data collection.
Skeptic-shipping: Seto Kaiba (from Yu-Gi-Oh!) and Chisame Hasegawa (from Negima!)
They're both skeptical about magic. They both have green hair in the first series and brown hair in all other media. They're both good with computers. They both come from series with exclamation marks in their titles. They're perfect for each other (although I don't know whether having a Net Idol for a girlfriend would help or hurt Kaiba as a president).
Fake(or Copy)-shipping: Copy X (from Mega Man Zero) and Barasuishou (from Rozen Maiden)
This pairing comes mainly from my team battle character choices in MUGEN (I don't play MUGEN much now that I have Melty Blood: Act Cadenza). They're both copies of someone: Copy X being the copy of Mega Man X, and Barasuishou being the copy of Kirakishou. They're both fairly unstable and willing to do anything to achieve their goals. Copy X would take over the world to save it FROM people who want to take over the world, and Barasuishou would toy with, use, and betray people, like Suigintou, to get Rosa Mysticas for her father, Enju. Also, as MUGEN shows, their battle skills complement each other. Their battle affinity might also symbolize their affinity in other aspects of life.
Prophecy-shipping: Vyers and Etna (both from Disgaea)
This is not a crossover, but still interesting. A Chinese belief is that if you can't be with someone you love then in the next life, you'll have better luck with a reincarnated form of that person. This can qualify as a prophecy. Etna loved Krichevskoy, however Krichevskoy was already married, perhaps Etna will have a better chance with the reincarnated version of Krichevskoy, Vyers (that is if she ever finds out who Vyers really is). Also, I'm quite glad I found them in Yu-Gi-Oh! card form.
Potential-shipping: Mega Man X and Karakuri Chachamaru
This pairing comes from the fact that even though X and Chachamaru are androids, they worry, love, and feel exactly like, and perhaps even more than, humans. Also both were hesitant in some situation. X hesitated to shoot the berserk mechaniloid's power generator in fear of hitting a reploid hostage and hesitated to shoot Sigma in fear of hitting Zero (both happened in the Day of Sigma in Mega Man Maverick Hunter X). Chachamaru asked if Evangeline could going easy on/spare Negi in episode 8 of Negima! to which Evangeline responded "You aren't programmed for mercy.". However, their hesitance, normally a weakness, is also the source of their great potential. X, eventually, defeated the God-Virus Sigma (though the Mega Man X game showing that has not been released yet), and Chachamaru's potential makes her "different" from her sisters, making her Evangeline's most favored android helper. Perhaps the concept of mutual love will further their potentiality.
