It took me a little bit to implement, but I changed the default file-naming conventions for MT using a method from Elise.
While there are varying degrees of implementation of this method, most weblogs I frequent had one thing in common, legible URLs. And while the legible filenames are a good boon to usability and minor help with SEO, the real reason I did this was to automatically organize all my entries in folders by category. A nice structural cohesion will make it much easier to manage this content in the future if I decide to delete entire categories, or anything else I can't think of right now.
So, for the code copiers here's what I put in place:
For the Individual Archive I used:
<$MTEntryCategory dirify="1" $>/<$MTEntryTitle dirify="1"$>.html
For the Category Archive I used
<$MTArchiveCategory dirify="1" $>/index.html