I have done the change: JQuery 1.9.1 and JQuery UI 1.10.0.
Seems Ok and stable in IE10/Chrome/FF, Admin menu is working for widgets, rules.
The useful ShapeTracing module is also working ok.
Main changes where on the obsolete method $("xxx").live(p1,p2) to replace by $(document).on(p1,'xxxx',p2)
then on the fact that jqueryUI now uses domains so data('autocomplete') became data('ui-autocomplete') or variant with item.
I attach here my new Orchard.JQuery module with the various .js changed (including some js from nawzet.ecommerce).
If somebody wants to try the changes and provide a feedback.
The code is attached to the issue here
Please do vote on the issue.