I've set several person-based filters to mark certain emails as "work" which are now yellow in color, certain (very few) as automatically "personal" (I separate personal from work email as much as possible for a number of reasons, such as the inbox dictating the default email signature my replies show), which are blue, and from my boss or my committee all come out as "important" in red font. I don't use the "priority" tags because they don't seem to further simplify anything. Also, I use the "order received" column instead of the 'date' column for order, as some people's screwed up backated machines get sent to me dated from 1969 and I have to search for them. Finally, I purge my inbox over to a "saved email" local folder every few days so I don't have to fumble through all that heft in what should be shiny and clean, our precious Inbox.
For my more neutral day-to-day email address inbox, I have a local saved folder, and a sub-folder for all online statements and receipts, things like that. It makes it SO much easier to find things.
I don't know how well any of this translates over to the newsgroup part of Thunderbird, because although I have some groups read on the program, I generally like dedicated reader agents like Xnews for it. That, and I don't read newsgroups anywhere close to as often as I used to before LiveJournal came and swept us all away.
By the way, if anyone else has any tried-and-true email tips/tricks, please let me know.