There are already many valid suggestions, here. Only very few, that would somewhat extend the basic idea of the product too much.
I don't want to explicitly double all of them, but the following two: (just because it may not be obvious how many people are in this situation)
1.
I am a Multi-Monitor user with different setups in office or when working from home. So I double #16/#17. A simple "autorestore" to what the user originally wanted, whenever a monitor is plugged back in would be nice. For some extra sugar, the user would be able to setup "rules"...
2.
Using a hot-key to bring the fences on top would also be nice. I am also burying my desktop under so many windows, which makes current fences really a limited experience.
And one, that I haven't seen in this list already, but I think it's valid enough to serve many people.
Imagine you have folders with many different file types, from which only a few are important and user-managed. The others are maybe temp files, files generated by some software (imaging VS .suo files and such). When looking at one such folder with a "portal", it might be nice to show only the important files. This would be easily doable, by setting up a filter, just like:
*.sln;*.prj