I'm making a cookie dough and forgot that I already had something in the oven. I prepared a baking sheet of cookies to go into the oven - but there is something already in there that requires another 45 minutes to an hour of baking (I can't fit both in at the same time). Can I leave my cookie sheets with raw cookies out on the counter until the oven is ready? Will this alter the taste of the cookies? (Will they get hard and yucky?) What about the cookie dough that is still in the mixer (and hasn't been formed into cookies yet)? Is there anything I should do to preserve it - i.e. cover the dough/cookies, put it in the fridge, etc?
You're going to have more issues with cookie-spreading than anything else, because your fat is going to get all warm. If you have a lot of fat in your cookies, you're definitely going to want to put the dough back in the fridge. If the dough is a hard dough, and you don't expect your cookies to significantly change shape during cooking, I wouldn't worry about it.
There is no concern for spoilage for an hour or less on the counter.
Are you talking about spoiling? Raw eggs and milk in the cookie dough going bad? I believe that what ever bacteria might grow is most certainly obliterated in the baking process. The dough was probably not dangerous from the start - handled properly, cold ingredients, etc. - so cooties have to be pretty mighty to get a foothold in one hour AND withstand 15-25 minutes in an oven. Come to think of it, I cannot recall ever hearing of salmonella poisoning being connected with baked goods. (Outside of eating raw dough).
Whether they slump from getting warm is another issue. See suggestions above.
It will depend on what's in the cookie dough
Butter, flour, and sugar is not going anywhere fast, it's the other stuff you have to worry about
I know people who regularly leave incomplete or complete dough for more than a day on the kitchen bench with no problems
Some cookies like ANZAC's go a little thin and crisp if left out for to long, but some people like them that way