Not so much a zone completion tracker, but there is a plug in called Deed Tracker that I absolutely love. I wish they would integrate it with the game, so it had full access to existing data. If you install it after you have already played through most content, you have to manually update all the deeds you already completed sadly.
And, there are some things (not a ton) that you can not complete if you missed it at the time you was going through it. I know there is a quest line in Rise of Isengard that you can't go back and anything you miss in it after you complete the over arching quest line because it involves a NPC you are escorting across the southern portion of the zone, and after you are done with him, you can't go back and do any of the quests you missed that required you to do it while you had him with you.
Like I said, there aren't a lot of these, but as a completionist, it really irks me when I find something like that that if you miss it the first time, you can't ever complete it later.