I use folders and colouring. I have a specific folder for all the clean/DI signals and few folders for either grouping of rythm/lead/acvoustic guitars etc. or for grouping of different sounds, e.g. I have a folder which bundles the high gain sounds and another one which contains the same guitar tracks with low to medium gain sounds. This way I can easiy compare by just switching complete folders to mute/unmute. Great for acoustic guitar versions as well.
Basically I always try to keep my core list of tracks which wil appear in the mix as small and condensed as I can. Sorting other tracks away in the folders so that they don't disturb. Important also (for me as a Cubase user) to keep the mixer clean in that way.