I organize strictly by function, as
Main (for Plugs you will use often)
-Mono EQ (all types)
-Mono Dynamics (Compressors and Limiters only)
-Mono Effects (Verbs, Doppler, etc.)
-Mono Signature (CLA, JJP, Kramer, etc. Signature)
-Mono Emulation (NLS, TT&T)
-Mono Extras (Meters)
-Stereo EQ
-Stereo Dynamics
-Stereo Effects
-Stereo Signature
-Stereo Emulation
-Stereo Extras
Alternates (for all other plugs you may or may not use.)
-Mono EQ
-Mono Dynamics
-Mono Effects
-Mono Signature
-Mono Extras
-Stereo EQ
-Stereo Dynamics
-Stereo Effects
-Stereo Signature
-Stereo Extras