I recently defeated a goblin invasion, however, my dwarves appear to be ignoring the goblin bodies and vomit everywhere, there are adequate refuse areas and they all have the labour enabled. Any ideas?
There are a few possibilities I can think of. First is the most likely. In the standing work orders. Are dwarves set to ignore outside refuse? This can be checked from the (o)rders -> (r)efuse menu. By default dwarves ignore refuse that are outside.
It is also possible that your dwarves are not allowed outside for some reason. You may have forgotten to cancel an alert that kept them inside the fort, or you could have set up some burrows that don't allow them to start tasks involving things outside the fort. It's even possible that you locked the doors and forgot to unlock them.
As for the vomit, (and blood) cleaning contaminants is a difficult issue. Cleaning is a very low priority job, and not all contaminated tiles are even considered for it (according to the wiki). Dealing with contaminants was enough of a problem that it is one of the more frequently referred to features of dfhack (the memory editor utility for Dwarf Fortress), that I have seen.