I use the traffic light system: Green, Yellow, Red. Green means great, yellow means whoaaa hold on we need to pause or renegotiate, and red means all play stops entirely and the scene is over. You really don't want to hear yellow and red is a pretty serious foul up. If gagged, the same idea is used with either holding up fingers (1 means fine, 3 means stop) or holding hands and squeezing. Its easy to integrate this system into play because you can just quietly ask 'color?' during play and continue. I think its also VERY important to have that medium level to check in at, because sometimes you can tell a scene is going downhill but if you don't hear a safeword, you assume you should keep going. Miscommunication 101.
Of course, this all depends on your level of play and your relationship with your play partner. I suppose some situations don't need such intense thought behind safewords--I love petnames over real names during vanilla sex, so if things get too rough, a quick bark of the Christian name ("DAVID! STOP!") usually does it.