I've been using WiinUSoft for a while now, but I noticed it has some sort of weird conflict with Uplay (Ubisoft's launcher for games like Assassin's Creed). Whenever I open the Steam overlay in a game and also have Uplay open in the background, the entire computer freezes up for about 10-30 seconds before the overlay becomes responsive, and the same thing also happens when closing the overlay. If I alt tab out and close Uplay (or, alternatively, WiinUSoft, but that defeats the purpose of using the controller then), the problem disappears altogether. This happens in any Steam game I run, as well as any Uplay game I run (so it's not universal to just one or the other, but all three have to be running to exhibit the problem). Uplay seems to have some sort of weird controller integration or something (you can use the A button on a 360 controller to start a game, but can't navigate with it, so it's more or less pointless), and I guess it conflicts with WiinUSoft's "not sharing" thing that was added recently.
Edit: I did some more testing, and it doesn't seem to really involve Steam at all. If I alt tab out of any Assassin's Creed game (sorry, those are the only UPlay games I have), regardless of Steam running, or bring up the UPlay overlay (basically anything that takes control away from the game) it freezes the entire computer for 10-30 seconds as I described above. When UPlay by itself is running with no game (UPlay or otherwise), there's no problem alt tabbing between applications.