Taken from the trade skill sticky:
Why do people fish in higher areas, then? The answer is easy: fishing normal fish gets you almost nothing of value. Fish, even the level 200+ ones, sell for a couple of copper to a vendor. However, fish are used in alchemy and cooking; so if you're spending the time to raise your skill and you can reliably fish in an area where the fish have a good niche on the market, why not sell them at the AH and make money while raising the skill?
Fish you'll want for alchemy:
Oily Blackmouth: http://wow.allakhazam.com/db/item.html?witem=6358
Firefin Snapper: http://wow.allakhazam.com/db/item.html?witem=6359
Stonescale Eel: http://wow.allakhazam.com/db/item.html?witem=13422
(Ohmikeghod added) Deviate fish: http://wow.allakhazam.com/db/item.html?witem=6522
As for an add-on. I use Fishing Buddy. Not sure if that will do what you want though. It keeps track of what fish you caught and where. Also, some other useful features as right click casting.