Here are a few I can think of off the top of my head that don't just pop up on the map:
Last Dom mission after you complete all parachute jumps.
I believe you have to call Tonya to get at least one of the tow truck missions to pop up. I called her to initiate the 3rd one, the rest came naturally.
The very last one is a Franklin mission and it's after you get 100% game completion.
One is for Michael after you buy the Sonar Collections Dock (northwest corner) as him.
One for Trevor (that starts a string of them) after you beat the game.
One after collecting all space ship parts.
One after collecting all letter scraps.
A long string of side missions that unlock only as Michael when you search the internet for Epsilon (see the Kifflom achievement).
The first bunch of Vinewood Souvenirs missions as Trevor are on your map as faint orange circles, which I didn't notice/forgot about for quite a while.
That's all I can think of. If you're only going for 100% game completion, you only have to worry about Franklin's side missions (aside from the one that unlocks after you get 100% game completion, obviously). Hope this helps.