Cooking down tomatoes I grow sauce tomatoes, roma and others. When they come in I blanch them, then run the thru a food mill. I then freeze the sauce in plastic freezer bags or cook it down into paste.  

I recently tried pulling out several bags of the frozen sauce to cook down into paste, I sliced the bags in a couple of areas and let them defrost over night on a cooling rack set in a tray.

In the morning, the bags had just the solid tomato matter and all the liquid was collected in the bottom of the tray. Very cool I thought. . but then. . . the question came to mind. . . . 

Am I losing any flavor or nutrients by just discarding this liquid or should it be cooked down with the solid tomato matter?
I definitely think you should cook it down.  I sometimes use canned whole tomatoes to make sauce by slicing them open and letting the liquid out, and combining that with the liquid from the can and whatever else (e.g, a bit of white wine).

I roast the tomato solids under a broiler with some sweet onion and garlic (starting the onion 5-10 minutes before anything else).  While that's happening I reduce the liquid by half, so it is a bit syrupy.  Exactly how much you boil off I guess depends on your ratio of solids to liquid.   The whole process takes maybe 20 minutes, then I combine the two in a blender.  If it's too thin or too thick, you can always reduce it further or add some water.

Roasting the tomato solids gives the sauce an enhanced flavour.  Credit where it's due: I got this idea from Alton Brown's "Good Eats" -- but I don't recommend the specifics of his recipe, which involve way, way too much vinegar, sugar and capers.  There's no strict recipe needed anyway; just add whatever you  normally would (or wouldn't).  Reducing a liquid and broiling tomatoes is pretty straightforward.