I have a load of virtual desktops running and I usually have one full screen application per desktop (so sort of like the Ratpoison WM but with an option to use it in other ways when needed). I want new windows to automatically be put in certain desktop numbers when they start up. What's the easiest way to do this?
You might want to take a look at the Devil's Pie tool; it is available in Ubuntu as package
apt-get install devilspie).
I, too have a lot of virtual desktops and a workflow that has me opening windows on different workspaces, but I've adopted an 'open and slide' approach with compiz.. right after opening an application, I use a customized shortcut to slide the new window to the appropriate workspace, then slide back to the previous workspace with another shortcut.
In my case, this is something like shift-ctrl-left arrow then ctrl-alt-right arrow.. very, very quick and I have full control over where they go every time instead of being locked-in to one configuration.