Instance List

Though I do suggest visiting as many instances as possible, it’s best to stick to the ones closest to the zones you are in and not making too much of an effort to spread out until your 50s. That means Alliance will do the Deadmines, Stockades, Gnomeregan and Scarlet Monestary. The Horde will visit Ragefire, Wailing Caverns, Shadowfang, Razorfen Kraul and Downs as well as Scarlet Monastery.
The Stockades should be done multiple times as it’s a really small instance. Scarlet Monastery follows the same rule. All others should only be done once, if at all. Uldaman is an optional instance that I personally don’t care much for. Zul’Farrak is a relatively small instance with good drops that should be done once. Mauradon should be repeated until you kill the Princess and get the Satyr’s Lash dagger. Once you get access to the shortcut, use it to do item runs as you can hit Landslide, Princess, Rotgrip and Tinkerer (in that order) all in one run that’ll last an hour. Sunken Temple should be done simply for the quests as the drops aren’t super for the level and it’s rather out of the way.

You’ll be spending a lot of time in Shattered Halls, Shadow Labyrinth and all 3 instances in Netherstorm just for the faction. Once you hit Honored with the given factions, these are the only places you can go to raise it further. You need revered to access the Heroic versions, which is a more dangerous version of the same dungeon with better loot. Currently the only way to gain faction with Honor Hold past honoured is Shattered Halls, so expect to see a LOT of it.