I'll usually wait until they've missed two turns. After that they can't expect you to wait. I wouldn't be angry if I missed two turns and my ally had taken advantage of it. Of course, I endeavour not to miss any turns.

If an ally misses a turn then they aren't holding up their end of the alliance and you should feel free to attack them, imho. This is especially true if a common enemy can stand to gain from his absence; there is no reason to let an enemy profit because of your allies NMR.

If they come back after one turn, I think there is still hope to continue the alliance. The ally should not be mad at you; it is their fault they couldn't get orders in. Likewise, you should still be willing to work with them; they didn't stab you; they can still be trusted.

If they have multiple NMR, then you must advance on them and after you've redirected your armies, it doesn't usually make sense to turn around again if they come back. Again, though, they have to reason to be upset with you.

i just had that exact situation in one of my games, i supported first turn but as next turn he would have lost his units to our enemy i took them instead but let him know what i was doing and to block me if he could. We were both safe that way. He took it really well and although i tried to get him to work towards our alliance again he kept not entering moves so ended up givin me his centres, he was really nice bout it tho.

think as long as u speak to them about it and allow them to block if they can, and to not be really cruel and take all their centres in one turn then its ok.

If an ally misses a turn he has broken the alliance since he clearly did not do whatever he said he would do and on top of that he violated the fundamental aspect of an alliance which is to play the game.

I write immediately to the player to find out what is going on, another reason to have an email address other than through the site so you have a greater chance to get feed back and can find out things like they are off the grid or whatever that may explain things.
If I do not hear back from them, then I treat it as a country that will probably NMR again under the phpDiplomacy system and act accordingly.
In other systems I would ask the GM to find a replacement player and delay the game.