At least once every session, run through your set as if it were for real. That means no stopping if someone makes a mistake, no chatting between songs and no toilet breaks. This process focuses each band member on how to optimize his role on stage. Your bass player may suddenly realize that she doesn't have enough time between song two and song three to turn on all of her effects pedals.
It's hard to tune in your guitar or tweak your tone while the drummer is warming up. Rather than setting up all together, do it in sequence. This way each band member gets a set amount of time alone to set up and make sure she is sounding great. While it may take longer before everyone is good to go, this approach cuts out the need for adjustments between songs.
Use a metronome to measure the tempo of each song. Then set the metronome to half the tempo, so you play each song half as fast. Mistakes can slip by unnoticed when playing fast, by playing each song in half-time you can really focus on nailing each part properly, without rushing. Playing half-time also helps improve feel and timing.
Sometimes technical problems happen and they're completely out of your hands, but your audience doesn't know that. Prepare for the worst by practicing as if the sound engineer was ruining your show. Do one run-through of your set with the worst possible mix you can come up with. Drench the vocals in reverb, turn the bass up too loud, turn the guitars down and put old sheets over the drums. This approach teaches you how to perform under pressure and without the perfect mix.
Devise a set of hand-signals during rehearsal, so you can communicate discreetly on stage if there are problems. For example, pointing your finger up and "drawing" a circle with it typically means "I've missed my cue, I'll come in next time around." Establish a clear hand-signal to communicate "turn your amp down," "turn your amp up," "slow down," "pick up the tempo" and "I'm not ready." The latter is very important as it prevents the band from starting before everyone is ready. Before every song you should all look at each other before beginning. If anyone is having technical trouble, then use this signal.