I tend to give each major thing I'm working on its own virtual desktop, which has a bunch of open browser and other windows. Each of the browser windows tends to have its own theme, too. (E.g. documentation for a particular framework, articles from a particular journal, a news topic, etc.) That makes it relatively easy for me to keep a handle on things. If I feel like I can't find things on a virtual desktop any more, that's my hint to clean things up a bit.
My biggest source of grief is session management between restarts. Firefox thankfully remembers the windows and tabs, but it doesn't reopen windows on the same virtual desktops they were on when it closed, at least under GNOME defaults. (Nor do the other programs.) That makes me do a lot of manual rearranging whenever it restarts, which is a pain. Other than that, it usually works well.
My biggest source of grief is session management between restarts. Firefox thankfully remembers the windows and tabs, but it doesn't reopen windows on the same virtual desktops they were on when it closed, at least under GNOME defaults. (Nor do the other programs.) That makes me do a lot of manual rearranging whenever it restarts, which is a pain. Other than that, it usually works well.