What is the most effective incapacitation?

There are numerous ways to incapacitate your enemies.

Here's a full list, ranging from the option with the longest duration of incapacitation to the shortest.

Bonus: Holding up an enemy at gunpoint and asking them to lie down will make them incapacitated indefinitely up until another enemy notices them.

However, if the base goes on full combat alert then they will get up.

To extend Linus Juhlin's answer, here are some of my observations:

Knocking an enemy down by throwing them (or kicking while they are on the ground or riding them over with D-Horse/D-walker) incapacitates for a lesser period of time than choking them.
If another guard finds knocked out guard, he rises an alarm. If another guard finds a sleeping guard, he just wakes him up (no alarm). If another guard finds a sleeping guard lying on the bed, he leaves him alone.
Knocked out/sleeping guards will NEVER come to (unless they are found by other guards), if you put them inside a portable toilet/garbage bin/passenger seat of jeep or truck/in the back of the track (you can load a whole base worth of guards in the back of the track - they will never wake up on their own!).
There is 6th ways to incapacitate your enemies - crawl to 15m or closer to the guard(s), open iDroid, go to music menu, turn on loudspeaker and play "afganian lullaby". If guard stays within 15m from you until the song ends, he will go to sleep. However, for some reason I've lost this tape after the first use (not sure if it's a bug or if this tape is one use only)