I want to ask to see when people feel its an appropriate time to record room tone on set. I typically wait until the end of the day to get all of my room tone recordings, even if I have to run around and record multiple rooms in a single location.
It's very important to establish a routine with the 1st AD (if there is one) as well, as he or she is most often the one who handles the scheduling of the day and calls the roll. On the first production day, make sure you let the AD know what you need (room tone as well as wild sound) so that recording room tone is an expected and integral part of the day. Asking for room tone when the G & E crew have already started to break down lights and rigging is usually too late.
Another point to make is that the presence of lights, camera and people will (usually subtly) change the room tone, so going back after the fact at the end of the day might not produce the results you need. If you have buzzy HMI lights during every take, that's what you'll need in your room tone. If they're not there at the end of the day, your recorded tone won't match.
Sometimes I ask that the Director to wait a few seconds after frame is called by the cam operator. If there's not enough time there. I ask for 15 seconds to 30 seconds of quiet before cut is called on the 'final' take of a scene.
The truth is room tone is mostly used from the takes themselves.. not from the separate room tone recording. The only time you really need room tone on a separate recording is if the ambiance is inconsistent or noisy.
Getting room tone at the end of the day usually doesn't work and a PITA to get.
I need room tone by microphone angle for dialog editing. I usually make fill with pauses between breaths, but if I can even get 10 seconds per angle, then I'm pretty happy.
A general room tone is really helpful when I'm backfilling MOS shots, then I don't have to try to make a fill from other takes, or the take prior.
A trick that I've been using on sets is pressing the record button, then acting like it takes 3-5 seconds to start my recorder. Everyone stays quiet for that long, so I get a little bit of fill
Flipstar gave a good explanation—I'll add that I've worked with a couple of directors who actually like to have a long silence on set right before the first take of a scene. It's a moment for everyone to relax and think about what they are about to do for the shot. Plus, no one is trying to "pack up silently" while you linger and curse them for every floor creak you hear.
Well usually what is expected from the director and the other members of the crew is roughly 5-10 sec of silence before the Director says ACTION and 5-10 sec silence after the Director says cut. That's what I request my director to do. Some of them follow, some of them just disregard it and think that everything can be FIXED in post. If you are freelancing and working mostly on indie films (like me), it completely depends on you on how seriously you want the director to take sound. Talk to the director about WHY you need the silence that you are asking for.