When i'm doing complicated shows with very little tech time, i try to get cue lists ahead of time from designers and stock up on post it flags - the kind that come in packs of 4 colors with a colored square and then a longer rectangular clear strip. Cue numbers and descriptions can be written onto the clear part, and the whole thing stuck on to any script page. Different colors for different kinds of cues (yellow=lights, blue=sound, green=deck/automation, red=cue light, etc. whatever works for that pruduction)
The advantage is that when you call a complicated sequence, then need to move the lights before the sound and the rail after the trap, you can literally pick up the cues and reorganize them. So after that preview when the director wants to try starting the music before the rest of the scene change, or cheating the trap open before anything else, those changes are super easy to make without lots of erasing. Less messy, and the color coding can be very helpful.
The disadvantage is the possibility of losing a sticky note, and the fact that if you make a copy you can't send pages with flags through an automatice feeder copier. I've never lost a note, and the exact cue location is still penciled in.
Sometimes i get paranoid and go through removing flags and writing in cues once the show is opened.
For long runs or shows that will be handed off, i use Matt's word based computer system. It's clean, easy to read, and handily archived electronically