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The main difference is in browser support: jQuery Mobile is on its way to supporting Windows Mobile, Opera Mobile, and almost any new mobile browser while jQtouch is only for Webkit. Also, jQuery Mobile works pretty well in Google Chrome from my experience if you're inclined to use a mobile app on the desktop for some reason, while jQtouch doesn't have animations on Google Chrome.

EDIT: And it's officially supported, meaning it's here to stay.

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In regards to your edit, jQTouch was acquired by Sencha and is now officially supported (and maintained) as well.

Though I prefer jQuery. But sencha also looks promising. They started investing heavily on web based mobile apps from the very beginning. Apart from sencha, Sprout Core also good player in this field and provide a quite complex framework for the mobile based development.

Was it really? I find that interesting, since jQTouch is much closer to jQuery Mobile in syntax than Sencha (which is a giant Javascript Object)

Yes there is a bifurcated development path. I prefer the HTML-friendly approach (JQtouch) as opposed to the monolithic Javascript (Sencha Touch)

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