After refrigerating cookie dough overnight, should i leave my dough at room temperature or go straight to the oven?
From the Fridge:

If you can scoop it (some doughs are too hard), go straight to the oven, though you will likely need to give them a minute longer baking time. This is actually beneficial for some doughs that spread a lot and some recipes actually call for a quick refrigeration.  I like to do this with sugar cookies (particularly snickerdoodles) as they don't get quite as spready.

Be careful when you say "for a while" though... most cookie doughs have egg in them and it's best practice to not leave that out for any length of time.

From the Freezer:

I also freeze dough (already scooped) and then bake a couple (or 12) at a time when I want a treat after dinner... or lunch or whenever I want a cookie... these can go directly into the oven and will similarly take a little longer to bake. Though, if you freeze the entire batch (without scooping), that won't be possible.

I do this regularly with homemade cookie dough and I've also worked somewhere that made the Otis Spunkmeyer cookies from the frozen dough balls and the directions clearly state to bake from frozen, do not thaw.

Here is a source that supports this:

StillTasty.com


  How to Freeze Cookie Dough:
  
  •  Wrap unbaked dough tightly with plastic freezer wrap or pack into a heavy-duty freezer bag or an airtight freezer container.
  
  
  When you’re ready to bake the cookies, thaw the frozen dough in the container in the refrigerator. (Thawing will take a few hours.)
  
  
  •   If you’re making drop cookies, you can also use this timesaving method: drop spoonfuls of cookie dough onto a baking sheet and place in the freezer until the dough is frozen (about an hour). Transfer the dough balls from the baking sheet into a heavy-duty freezer bag or an airtight freezer container.
  
  
  To bake the cookies, simply place the frozen dough balls directly onto a baking sheet and bake a few minutes longer than indicated in the recipe.
  
  
  •  If you’re making sliced cookies: form the dough into a log, as directed in recipe. Wrap tightly with plastic freezer wrap or place log in a heavy-duty freezer bag.
  
  
  To bake the cookies, you don’t need to thaw the frozen dough log — just slice off what you need with a sharp knife. Bake the frozen dough for a few minutes longer than indicated in the recipe.
  
  
  •     Use frozen cookie dough within 4 to 6 months for best quality.