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0f7b58d
(Get the code!)
I just confirmed that, if I unmaximize all my windows, and place them toward the center of their respective viewports, using Super-Numeric will again properly switch to the correct viewport as well as raise and focus the selected window.
I routinely change screen resolution from 1680x1050 to 1280x720 and back again (to clone to a 720p projector). Also, excepting Terminal, I generally keep my windows maximized. Changing resolution like tends to move all my windows back to viewport 1 (I use, probably like most folks, a 2 x 2 viewport grid). I've been using Alt-Space -> Move Windows to Another Workspace -> Workspace <#> to put the maximized windows back the various viewports where I like them. I've noticed, though, that if I then unmaximize these windows, they often then are just barely on the same viewport and occasionally even on a different viewport. I think this may be the heart of the problem, or at least part of it.
It seems like Unity is determining a window's viewport based on its unmaximized state and ignoring it's location in a maximized state. More generally, it strikes me as a design or implementation flaw to be able to have a window unmaximized on one viewport and then, if you maximize it, it ends up on a different viewport. I can understand how changing screen resolutions might be an unanticipated way of getting into this state, but I think that this is something that the Unity Panel should handle more intelligently.
I also use Compiz' Expo view a lot to reorganize windows, but I don't think that's the problem. Others have talked about snapping windows as being related to the problem.
It seems to me that a picture is emerging here: Unity is not doing a good job tracking the relation between window geometries and the viewport(s) upon which those geometries fall. Expo, snapping windows, changing screen resolutions: These all seem to lead Unity to get "confused" re: the mapping from window to viewport and vice versa.
Other bugs I've seen that seem a part of this "cluster" of issues: Bug #799552, Bug #802664, and Bug #807442.