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I always put everything into one file. I just like the integration, and I tend to think of my life as one big thing without too much distinction between work and home, etc.
The tree can grow very quickly, but I think the beauty of the logical links is that you can have alternate pathways into your data constructed in the most accessible places. I tend to put action-oriented material at the top of the tree, and reference material at the bottom. That way I can always jump to the top of the tree and be near things that require work.
I also use a combination of tree hierarchy for organization and saved searches for quick access. For example, I have an "All Projects" search that will list all project items. I can then quickly jump to these projects no matter where they are nested in the tree and I add task items below the project item. I use several saved searches to pull together task lists based on different criteria (Overdue, Due Today, Due Within 1 Week, Calls, Off-hours, Errands, Waiting, All Open Tasks, etc.).
To me, the combination of searches and linking makes me not worry about the overall size of the tree too much. I do find that I need to conduct more specific searches as my database grows larger in order to get a workable set of results to deal with.
It may be obvious, but I find that learning all the keyboard shortcuts really helps with this kind of software, especially when you need to jump around among the various panes.
It's always fascinating to me to learn how others organize, so I hope we'll get some more input.
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