The simple answer is to be in record when things happen. However, that can sometimes be not so simple, especially when taking into account reels of tape and such.
I have never lost a note in the studio, because when a new group of musicians is setting up, I go to great lengths to get us all on the same page about the recording process. I explain that I will put the system in record, and I tell them what specific language I will use to cue them. This is really only "director speak", and I acquired it from years on the road doing broadcast music programs. It doesn't matter what you say, only that everybody knows what you're going to say.
Occasionally I have worked with players working up pieces who wanted to keep tape rolling, but they knew how to move quickly between takes and not waste space on the tape. With hard drives, this is not an issue. Just put it in record and let it run.
Live, I have only lost a single song, but not due to my mistake, but due to an A2 who thought he knew better when I called "roll tape!". He thought I made the call too early and he delayed just long enough to miss the intro to an Aerosmith song! Arggg! I could have killed him! But the band was way cool and just acted like nothing happened.
Last summer Jonathan Burtner, Bill Urik and I did a live recording in Atlanta. We were only supposed to capture the fifth song of each artist, but some artists began moving their sets around and not telling us. So I decided to start making the roll tape call earlier. One act was adamant that she would tell us when to record. I knew she was going to screw it up, so I told the guys to roll during the previous song. Of course she forgot to look over and cue us to record until the drummer was actually playing the intro.
Bill