My sorting scheme is as follows:
Minifigure box #1- (Star Wars) Clones/Senate Commandos, Imperial troopers/Officers, Jedi, Sith/General Grevious/Imperial Guards, Battle Droids, Snow Troopers, Ewoks/Wookies, Rebel troopers, Elite CIS troops (Super battle droids, Droidikas/Spider droids), SW Civilians, Assasin droids, Bounty hunters/Other.
Minifigure Box #2-(Castle themes) Prince of Persia, All horses, Crown Knights (Fantasy Era), Trolls (Fantasy Era) Dragon Knights (Kingdoms), Elves/Dwarves, Lion Knights (Kingdoms), Knights Kingdom, Skeletons, Royal Knights, Other.
Minifigure Box #3-(Miscellaneous) Indiana Jones, Spider-man, Space Police, Rock Monsters, my one Harry Potter minifigure, and any figures that I need to keep together for current or future projects.
Minifigure Parts box-(All figures not in other boxes or on display) Hair, Helmets, Modified/Special heads, (Aliens, any coloring but yellow) Medieval/Warrior faces, Modern faces (Anything with glasses, microphones or something which is a modern invention.) Other faces, Black legs, White legs, Blue legs, Red/orange legs, green legs, other legs, Special legs (Dresses), Special figures (Mostly Robots), Civilian torsos, uniforms (Firemen, Police, Cameramen) Soccer uniforms, Sci-Fi torsos, adventurer torsos, loose medieval torsos, other torsos.
All other minifigures are on display with their respective sets. (LOTR/DC Comics/Marvel/POTC)
Bricks are separated like so:
Technic bricks, Technic other, Minifigure accessories, Minifigure Tools/Weapons, Connecting bricks/plates and hinges, Windows/Doors, Tires, Bionicle, Foliage, Brick Separators, Wall panels/URPs, Miscellaneous, Black/Brown/Dark Grey Wings/Round plates/Round bricks, Black/Brown/Dark Grey bricks, Black/Brown/Dark Grey plates, Black/Brown/Dark Grey slopes, White/Tan/Light Grey bricks, White/Tan/Light Grey plates, White/Tan/Light Grey Wings/Round plates/Round bricks, White/Tan/Light Grey slopes, All other plates, All other Wings/Round plates/Round bricks, All other slopes, "Cool" bricks (Blue, Green, Purple) "Warm" bricks (Red, Orange, Yellow) Baseplates, and finally Jet engines/helicopter blades/special flying vehicle parts.
It's really a lot less complicated than it sounds, trust me.
The only problem is that while all my minifigures are sorted, only about a third of my Lego bricks are sorted....