Stargate SG-1 and Animorphs...hey, they both already have alien parasites...
I've read one of those, but I don't think it was ever finished. I think the premise was that the stargate malfunctioned and somehow switched Jack and Jake's bodies. Oh, and Daniel Jackson was a Controller and the Yeerks and Goa'uld were making some sort of alliance. I can't find it anymore, unfortunately.
I think the idea might work. I can't write fanfic very well, but if I could I might have a try at it. One thing I'd like to see in an SG-1/Animorphs crossover is how Ellimist and Crayak would fit in with Stargate's "Ancients".
I'm actually planning out a Pokemon-based sprite cartoon series and I'm trying to see how I might fit in Yeerks and/or Andalites (the series backstory explains how aliens came to be and their relation to Pokemon and humans on Earth). It's not a conventional Pokemon story at all.
One particular "scene" I was thinking about takes place in roughly 2001 in the series' timeline and involves the Team Galactic Commander Saturn (who is actually a Goa'uld System Lord, also named Saturn) trying to continue the former leader Cyrus's plans to become a "god." He uncovers the stargate which is buried somewhere in Sinnoh and is about to send a message to his fleet when one of the humans in Sinnoh's intelligence department (who is, of course, after the guy) reveals that he is actually an undercover Andalite sent to investigate possible Yeerk activity (the Yeerks, as it turns out, are operating in Kanto and feature somewhere else in the story).
As it turns out, the Pokemon world is both a blessing and a curse to both the Yeerks and the Andalites. Pokemon (who are explained to be a bit higher up on the sentience ladder than real life animals, with some - i.e. Alakazam - even being more intelligent than humans) could provide the Yeerk forces with a very powerful army of Controllers as well as powerful morphs for Andalite warriors. The downside being, of course, that some Pokemon (and humans, too, apparently) have some degree of psychic powers and could see through any Yeerk or Andalite disguise. Overall it's a nice concept, and I'm sure Pokemon/Animorphs has been done before - just not done how I plan to do it.
Whew, think I got a bit carried away there!