I vary the number of chat boxes I have open. Raiding gets one more, sometimes two.
Main chat is Say, Tells, Group, Fellowship, Guild, Raid, Shout, Auction, OOC, #channels, emotes, Pet Responses, /who, Other. Also melee: Disciplines, NPC Enrage, Others' Deaths. Also spells: Failures (extremely useful filter, this encompasses resists for all spells, but also mitigation for slows, indicating that slow landed) & Worn Off. Clearly, I do most of my playing from that window
I have a window for melee. Others' Melee (I have others' misses off, but that's it. The collected data for parsing is awesome), Pet Melee, Melee warnings, etc etc. This window also has Non-melee damage, so I suppose it's more accurately called the "not my damage" window. This window is usually kept quite short, since it's only important most of the time to see whether or not it's scrolling. Keeping a window like that minimized is a good way to client crash yourself when you restore it, btw. Don't minimize the melee window.
Window 3 has all the spell stuff going on, Other's Spells, my dot damage, my melee (hits, misses, hitting me, missing me). Focus effects have been turned off for a long time.
When raiding, the guild healer channel gets its own window, since it turns pretty darn spammy during events.
A fifth window pops up during any scripted or simon-says type encounters, for just the "Other" filter.