To help avoid this irritation, Wrath of the Lich King will be introducing something currently called 'championing.'
The term will likely change before Wrath's launch, but that's what it was called at The Worldwide Invitational's Dungeons and Raids panel. With this mechanic, you'll be able to gain some reputation with some factions outside of that particular faction's dungeon cluster when wearing a certain item, most likely a tabard. For example, you may want Honor Hold rep but don't feel like running Shattered Halls all week long. You can equip this item and go into Steamvault, and gain reputation with both the Cenarion Expedition and Honor Hold. If you run Shattered Halls with this item equipped, you gain a little extra reputation along with what you would have normally gained.
This new mechanic can very easily be seen as 'dumbing down' faction and reputation, but I'm pretty excited. Most of my friends wanted to hit me in the head with a brick after our tenth Shadow Labyrinth run, but they were kind enough to keep doing it for me. This way we can all work toward our own goals, while still helping eachother out. My pocket tank could keep tanking for me to help me acquire my hammer, but she could have also tossed on a Keepers of Time tabard and gained reputation toward her Timewarden's Leggings. I did use Burning Crusade factions as examples here, but don't get confused. This will be implemented in Wrath, and not retroactively for TBC. As far as we know, anyway.