It's totally a personal thing but for me it's very useful to stick to a regime so you can go quickly to the right tracks(s).
I've always coloured my tracks and clips:
(B=background, F=foreground)
Drums and percussion - B red F white
Bass - B browns F yellow
Keyboards - B blues F white
Synths - B purples F white
Strings - B greens F dark blue
Brass - B yellows F dark blue
Vocals - B grey F purple
Rhythm guitars - B light pinks F blue
Lead guitars - B vibrant pinks F blue
Oh, and I usually sort them top to bottom:
- Drums
- Percussion
- Bass
- Keyboards
- Synths
- Guitars
- Strings
- Brass
- Vocals
I put all MIDI tracks in a MIDI folder, audio in an Audio folder and mixes in a Mixes folder.