Gundam SEED [Destiny] and Excel Saga...
my brain is bleeding just imagining that, even worse is for me its always a 3-way-tie with Chobits for my favorite so the idea of Chii, Excel and Kira meeting just makes my head hurt. Seeing as in the original japanese Lacus and Chii have the same voice actress [Rie Tanaka] i think Kira and Hideki would be very confused, though i think Chii would get a long well with the Eternal crew, Sumomo and Haro would get along well and Minoru and Waltfeld would do well to meet each other [knowing him would explain the cross-hacking fight with Gilbert at the end of Destiny] Hibiya and Murue Ramius would be able to exchange sad stories and who knows, Mu and Chii could work through their parental issues. and i'm sure Shinn would be happy to meet people more depressed than him.
on the same hand i guess Meer and Excel together would be pretty funny, Gilbert meeting Lord Illpalazzo would just be an intellectual squee moment for me, those two madmen exchanging world conquest plans. Hyatt and Rey/Ra could talk about how much it sucks to have a degenerative fatal disease and what its like to die constantly. the two guys from the F City, F Prefecture self-defense force could have a very deep discussion with Athrun about what its like to be an absolute failure with women.
Excel meeting Sumomo would probably drive Kotoko to self-terminate. Hideki would be horrified by Hyatt vomiting blood and dying a lot. Ropponmatsu 1 would probably fit in fine [she practically is a persicom already] and 2 would fit in great with Sumomo as well [well as long as she doesn't fall in love with and then rape any other girls like she did poor Excel (though i'm sure Hideki wouldn't REALLY mind *wink*)]. Ueda would be happy for all the help that the Across girls and the Ropponmatsus could provide...
Nabeshin v.s. Kira in the Strike Freedom METEOR equipped would be the most epic battle in the history of time, NABE-HAME-HA going up against a mega-particle cannon, two linear cannons, two beam rifles, two anti-ship beam cannons, 8 dragoon funnels and 10,000 missiles would be awesome.
Key... a questionably bi/homo-sexual man who walks around in in bondage gear and buttless pants and whp plays the guitar and ocarina... him versus Kira in a Bisho battle, then add in Chii for a costume battle.
yeah, i almost want to start a fanfic of a Tsubasa-like variet with these 3 universes clashing, but being as i never did my ToS x EVA one, its doubtful i ever will.
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Kira = Cuteness.

Remember kids: if you touch Lacus Kira will beat you to death with meteors.
"If something truly was a problem you'd take the actions needed to change it."
-my personal motto