Many things are accomplished through farming instances and the most important one with the advancements of the Burning Crusade expansion is reputation farming. Rep farming is needed by many new factions for some wondrous items and gear as well as some attunements for instances pertaining to that faction. While rep farming may be a major part there is still a great deal of good lot so grab a group and get ready to slay some bosses.
Azeroth
Azeroth has existed for many centuries and fallen age-old societies are ready for your looting pleasure, Dire Maul being one of great interest.
Deadmines (levels 16-22), Ragefire Chasm (levels 12-22) (20 Gold per hour)
http://www.thottbot.com/z1581
Target Items: Boss Loot and anything else that drops (Greed Run)
Location: Deadmines and Ragefire Chasm are usually farmed by alliance or horde characters at least level 40. At 40 a character can solo these instances and take all loot for their own to either auction off or disenchant for great profit. In each of these instances there are a couple of BoE blue items, but sadly they only have about a 1% rate in dropping, but could be sold for 15 gold or more!

Scarlet Monastery (levels 33-40) (60 Gold per hour)
http://www.thottbot.com/z796
Target Items: Chain of the Scarlet Crusade Armor Set
Location: Scarlet Monastery is another place of interest as it can be fairly easy to solo at level 60 and above. In Scarlet Monastery’s graveyard there is always a chest that spawns in the torture chamber and this is a great target for higher level rogues. Other can simply progress through the different areas of Scarlet Monastery and rack up the gold from the cloth and items which drop from its mobs inside. When farming Scarlet Monastery make sure to keep an eye out for the armor set “Chain of the Scarlet Crusade”, below is a detailed chart to let you know where the armor pieces drop and their rate. Not all of these items are BoP and can be auctioned. If you are farming Scarlet Monastery for things like cloth or items to DE this chart will show you some items that may drop and are things to keep your eyes open for.

The armor set bonuses are as follows:
2 pieces equipped: +10 Armor
3 pieces equipped: +2 Defense Rating
4 pieces equipped: +5 Shadow Resistance
5 pieces equipped: +15 Attack Power, when fighting undead
6 pieces equipped: +10 Hit Rating
Dire Maul (levels 56-70) (80 Gold per hour)
http://www.thottbot.com/z2557
Target Items: Thorium Ore, Boss Chest Loot
Location: Dire Maul East is a Thorium Emporium since after killing its last boss you have access to 2-3 Rich Thorium Veins. A strategy of great interest when it comes to Dire Maul is a stealth run. Stealth runs include usually 2 druids and 3 rogues stealthing their way past all enemies to the last boss of the chosen wing, killing it, and taking the boss loot chest that spawns for great profit. Each boss you skip in an instance with a boss loot chest at the end adds more loot to that chest. This is why it is essential to skip as many bosses as possible unless someone needs that boss specific loot that may drop from the kill.
Strategy: Usually a good set up for this technique is 1 restoration druid, 1 feral druid, and three rouges of any chosen spec in talents. This way you have a solid tank, proficient healer, and more DPS than any 5-man boss can withstand.

Outland
Outland instances were built for farming and you will be spending a lot of time within them doing just that. Rep farming is a major part of end-game content here and needed to purchase some factions advanced items. There are also great equipment sets along with other loot waiting to be pilfered for your use or profit. Once you achieve revered with an instances governing faction you can buy keys for the instances Heroic difficult mode and is your gateway to even greater treasure and gear. Time to fill our pockets with gold and make sure the denizens of Outland are aware of our deeds.
Outland instances are rather straight forward and currently difficult to farm solo. Grab a group and start running dungeons you need reputation for. There is however one trick for rogues you should be aware of.
A trick for rogues (level 70, flying mount required) (200 Gold per hour):
http://www.thottbot.com/z3848
Target: Treasure Chest
Location: The Arcatraz, near first boss.
Strategy:
There is a chest waiting for your taking in The Arcatraz. This instance requires a flying mount to reach and either the key or a max level pick lock skill to enter. The chest may also be locked so remember to bring your Thieves Tools. Upon entering the instance go into stealth and UN-equip your weapons and armor as these will take damage when or if you die.

Go forward, wait beside the left hand side of the door you see the Protean mobs coming out of, simply wait for an opening and enter that hallway sticking to one side or the other all the way against the wall. Progress to the second section and wait for another opening. The go into the room ahead and be careful as Proteans can spawn on top of you. Go into the next hallway dodging the fallen guards and into the next room.

Simply dodge the mobs here, on the far side of the room near a floating eyeball creature you may see the chest, this is the one we are after. If it is not there exit the instance and reset it. Ok now go onto the walkway that will take you to the next floor, usually there is a protean running up and down this ramp, when it is gone come out of stealth, sprint, and jump onto the rail next to the wall. Enter stealth or vanish if need be. Now line yourself up with the chest, go to your left a little and it may look like you will jump onto the ledge above the chest, jump, and take yourself back into the corner.
When in the corner wait for any Proteans to pass if need be, come out of stealth, open chest. You will get agro but nothing will be able to attack you. Simply keep clicking on the chest and when you exit combat (this will happen automatically after a few seconds, maybe up to a min.) you will open the chest, get your loot, and if you can vanish. If not just die because the mobs will now teleport to your location… Repeat…
You can only try this 5 times per hour as there are limits on instances you can enter. This chest almost always has a level 70 green but sometimes a level 68 or 69 blue, always has a little over 6 gold, sometimes it contains potions, and most of the time there will be a high level gem such as Star of Elune or Living Ruby. Enjoy rogues, as this can be rather difficult and takes a good deal of patience but the rewards are well worth it!