It's a small thing, but

Take it out.  The micro is communal properity for the employees.  It's not their personal property.  Besides, it's unsafe to nuke something and walk away.  If they were home, it's one thing but not in the work place.

Some people at my office are notorious for leaving their food in the microwave and get all bent out of shape when it's relocated so someone else can use the microwave.

My thought is if  you leave it, you're subjected to be moved.

I am with the others.   Personally, if I forgot something in the microwave, I would not be offended if it had finished and someone took it out for me so they could use it.   I dont usually walk away from it, but sometimes I will to go to the bathroom which is right next door to the kitchen at my work.   But I usually go right back in and get my lunch.   I will admit though, there has been once maybe twice that I have walked away and gotten distracted and forgotten about my meal.   It was not until the end of the day that I realized that I had left it in the microwave.   I am a constant multi-tasker and so, if it is going to take more than 2-3 minutes to complete, I might go do something in the mean time.   I am not one to be able to sit still and watch my food rotate in the microwave.  I can think of so many other ways to better use my time, but I do go back and get it immediately usually.   However, since I eat 6 small meals a day... the times I use the microwave are usually times just before or just after everyone else has used it.  

I would set it next to the microwave and cover it with a papertowel.

I think I like this option.  That way, if they come back it looks like their food was at least handled with care.

Maybe I'm projecting how I would feel if I found out somebody had been messing with my food behind my back.  I would be totally paranoid about eating it.  Everybody doesn't practice good hand hygiene.

IF you like the co-worker: take the food out, nuke yours, then put theirs back in.

If you DON'T like the co-worker and the microwave room is not under surveillance, put a booger in their food. It's juvinile, I know, but it's a fun alternative.

Good grief, I can't believe how many are getting their panties in a wad over this.  Just take it out and set it aside.  If they're not back when yours is done, put it back.  If they walk in, they walk in.  No big deal.  You smile and say, "Yours is done." 

I use the microwave at work all the time and almost always go to the restroom while mine is nuking.  I'm usually back in plenty of time, but if not, then I would expect it to be taken out if someone else needed it, and I would certainly not be offended.  And I certainly don't think it's rude...3+ minutes is a long time to be staring at a rotating meal, and that's what it would be for me.  As a sub in the one building, the regular teachers are not very welcoming, so to sit there with them while waiting would be awkward.  Much easier to leave for a couple minutes.  

OK.  I laughed out loud at this one.

leave it in and nuke it again with your food :)
That way you never touched it :)

If their food looks better than yours, eat theirs and leave yours for them...  just sayin'