I tend to partition them into windows once the favicons go away. Otherwise mostly based on the ordering (which I adjust regularly).

Much of the time they are effectively a queue of things to review/skim/familiarize myself with while I'm authoring some code or a design doc. The ones with different favicons tend to be things like bugs where I owe an update, so I scan through them regularly (I'm extremely forgetful when it comes to lists of things to do).

Honestly I know how tree-style management would go for me: I'd group a bunch of things together in a tree and forget about them, largely defeating the purpose of having kept the tab open for me.