I have a good few books on stretching and flexibility. There's tons of different muscles and stretches to do, it would take me a good few hours to stretch every muscle.
Or am I missing something? Is there some sort of secret for stretching the whole body? Is it even necessary? I assume yes as you don't want imbalances as a result of only stretching some muscles.
You're correct: a full repertoire of stretching could take hours. The good news is, any exercise that works through your full range of motion (which, itself, is highly variable from person to person, and even from moment to moment) will at least maintain your range of motion, if not improve it. A lot of resistance training actually includes stretching within the exercise. A good example is the Romanian deadlift, which both stretches and strengthens the hamstrings (sufficiently enough that after about a year of doing these every week, I recently switched over to stiff-legged deadlifts starting each rep from the floor, because it was either that or start standing on a block to do RDL: this being without doing any consistent flexibility training). My calves have also gotten more flexible from doing calf raises this year, and a few years back squats and bench presses improved my calf, glute and pec flexibility (which I've since maintained by continuing to do those exercises).
In general, most people have exactly as much flexibility as they need todo the things that they do. If you're learning to do something new and need more flexibility for it, then that's a good time to do specific stretches for it. If you have a muscle imbalance or need to do rehab and that includes direct flexibility training, then that's a good time do focus on stretching specifically. If you just feel like stretching, then that's (usually) a good time to do it. Beyond that, I wouldn't worry about it too much.
A comprehensive stretching program could have you there for hours, but you can do rudimentary whole body stretches pretty quickly, they just aren't as effective at anything specific.
