For example, GIMP works without any issues. And the productivity boost is tremendous, for me it's very hard to work on anything else. I barely encounter programs where it does more harm than use.
Especially having multiple desktops with different names allow me to localize windows so much quicker than looking through a dozens of terminals manually.
Right now, I do have: 1 mail, 2 web, 3 gimp, 4 chat, 5 notes, 6 terminal, 7 ssh cluster
I use StumpWM, and for the few applications that this becomes a real problem it is possible to run those in a floating windows group that works just like a minimalistic non-tiling window manager. I think this is a common features of tiling window managers.