I was doing the same last night and have come to the conclusion that I am going to thin out my huge random collection and give those I don't use to some of my fishing mates that don't tie their own.
Of my collection I probably only ever use about 5%.
Now I am starting to float tube I am moving to water proof boxes so things may change yet again but at I have the following:
Dries - use a richard weatley - one side foam and the other glass compartments.
Buzzers - A floating foam box
Caddis imitations - A medium black plastic job
Traditional Wets - a medium red fox box (don't like and may replace)
General nymphs - A medium black plastic job
Lures - a small wooden box (rarely take it with me)
I now have a floating zippered foam wallet that I use for a mix of those flies I am most likely to use during the session...keep it handy while the others are tucked away.
Also have a couple of wooden storage fly chests
A large black plastic box for my seatrout selection
A large fox box of salmon flies (don't like) and two loose boxes or large tubes and mini tubes.
Also a couple of old cigarello tins, foam lined, that I used for my river flies - mainly wee spiders and the odd goldhead (I'm not much of a trout river man

)