the the best option that i could think of would be to visibly shrink the multi monitor window down to a single monitor unitl it comes back into focus or the user swaps that monitor back to the previous workspace and then have it convert back to it's normal size.
a shrink/grow animation similar to the orange box when you're full screening or half screening a window by dragging it to the top or one of the sides of the screen wouldn't be so bad.
i've got no ideas about possible solutions for the different sized monitor problems. though i don't know of a setup using different sized monitors which doesn't have those problems.
my brother used to use different sized monitors. he's a windows user so he didn't have the option of workspaces but he had some of those kinds of problems as well when simply dragging a window from one monitor to the next.
heck, i even had some of those problems a while back when swapping between a 1920x1080p TV and then swapping it back to my old 1600x1200 monitor later on. it would open hulu desktop in a resolution wider than i was using and wouldn't let me shrink it down enough to fit my monitor without editing the file that kept track of the huluDesktop window size.
i don't know that there is a good solution for that other than not using different sized monitors and that's not really even a solution to the problem... especially if you've already got different sized monitors.