All cars can be stored in garages. The standard car will always reappear near the safehouse.
I had times where my stored car disappeared and got replaced by my standard car (both Michael and Franklin). Of course, there is a possibility this was because a mission replaced said car early in the game, or I genuinely forgot the car somewhere else (hopefully the latter of the two).
The garages not tied to the safehouses work the same way, but you are able to access a special car (I have Special Edition, but this is likely for every version of the game).
Air fields should work the same way, unless they work like helipads (can be tested with another plane). Helipads MIGHT be able to store more than one helicopter. I am not sure of this.
After the IAA abduction mission, I flew back to Trevor's airfield/helipad storage area with the Frogger helicopter from said mission. I landed nearby, since the spot was already taken by another Frogger, however, before this mission, the helipad was empty: this was my first time flying a helicopter.
Going near the helipad, the game gave me the option to "switch helicopters" with the right DPad, however, the only choice available was the Frogger. This got rid of my other Frogger, right before my eyes.
I flew around with the spawned Frogger and came back, to see a completely different Frogger spawn. So I think that option was to set which one spawned. No other garage so far has given me that option, and I do not know how to add more helicopters to the spawning option.