It hasn't been updated for a bit, but there's an addon called 'Everyquest.' It should keep track of quests you've done and let you know where the remaining ones are. It was updated at least at the start of Cata, so should be fine for older content - you may just have to enable it as an out of date addon if it doesn't show up.
You are most likely missing the Kirin Var quests or the outlying Area 52-Goblin quests. The link I posted lists all of the problem spots in the comments section.