I have a number of quests that say "Collect bounty from..." and I can't collect it, so they hang there unfinished.

Nor can I tell what quest it was from to command line complete it. I thought if I could get a reference to all of the currently active quests, I could loop through them and see what stage each was in, and then look at my quests and see which ones are really bad.

Does this make any sense?

I found QuestScript
http://www.creationkit.com/Quest_Script
And looping through.
http://www.creationkit.com/Complete_Example_Scripts#Cycle_Through_a_List_of_Objects_and_Perform_an_Action_on_Each_Object.28FormLists.29

While you could add all (vanilla game) quests to a formlist and roll through them, I am not sure it would help.

Those sound like story manager based radiant quests:

CK -> Object Window -> Character -> SM Event Node -> Script Event -> Stacked Branch Node : WEBounyCollectorBranch

Which all resolve to the WEBountyCollectorQST. You could try in console:

StopQuest WEBountyCollectorQST

but I dont know if it will do any good.

HAHAHAHA Thanks Dheu. They are story manager quests, by Skald. I found a command line that promises to fix the issue but as a side note, I now understand how the quests are created. For anyone looking too, there's a mod here:
http://skyrim.nexusmods.com/mods/13903

That promises to fix the issue.

I've looked at all of the quest commandline options and it seems they do what I need but the ones I'm after by Skald say completed.
That mod does not complete the broken (already progressed) quests just to be clear. It was not meant to.