The Shattered Hand Clan of the orcs and trolls
Even though Garona was half-draenei, and did have a few strong relationships with humans, she was definitely a part of the Horde first, and identified herself primarily as an orc. She must have felt this was her only option, particularly back in the days when the old Horde was still made up of orcs only, and controlled by the Burning Legion.
In those days, the Shattered Hand clan was among the most bloodthirsty of the clans in the war with the draenei, and again very eager to take the war to the humans in Azeroth. They were named for the gruesome practice of self-mutilation they used to follow in those days. Following the Second War, however, the clan was split in two, with those remaining on Draenor under the command of their old chief, Kargath Bladefist, and those stranded in Azeroth eventually following Thrall when he founded the New Horde.
Those that follow Thrall now are the ones who carry on Garona's legacy the closest -- as the guild of spies and assassins among the orcs and trolls of the Horde, it is their responsibility to train the next generation of rogues in service to the Warchief. The ravings of one rather insane member of the Shattered Hand indicate that there may possibly be some plot amongst them to assassinate the Warchief, but then again, that may just be mad ravings without any substance whatsoever. If your rogue is a member of the Shattered Hand, you can choose whatever loyalties strike you as most interesting.
Sylvanas' elite guard of rogues is among the best in Azeroth. Members of this guild, called the Deathstalkers, have a number of advantages that few other groups can claim: They never need to eat, drink, sleep, rest, or breathe. They have all the single-mindedness and focus of a machine without any of the drawbacks. They have incredible willpower, and can stay patiently focused on their goal indefinitely, whether that means they staying underwater, or disguising themselves as corpses (which... they are).
That reminds me, the only downside I can think of as a Forsaken rogue is: would you stink really bad? Would anyone you spy on always wonder where that rotting stench is coming from?
Anyways, the loyalty of the Deathstalkers is even more questionable than that of the Shattered Hand. [Spoiler alert! Stop reading now!] The demon Varimathras has for a long time been master of the guild, and it stands to reason that many of the rogues and spies under him would have sided with him in his betrayal against than the Dark Lady. Generally speaking, however, the Forsaken are fiercely loyal to Sylvanas, and it's more likely that any player's character would remain loyal to her. In any case, even if you wanted to betray her and side with Varimathras, there's no way you could actually do so in the game; the quests in which this issue arises require rogues to kill the demon just like everyone else. On the other hand, perhaps a traitorous character could just stand by and watch while her friends do him in, knowing that she cannot save him, and wishing she knew who his true master was. [This spoiler is now complete. You may continue in your regularly scheduled blissful ignorance.]
The Deathstalkers were originally a group of human bandits who followed the "Bandit King" Blackthorn during the Third War, until Sylvanas decided that they ought to serve her instead of running around terrorizing people. She had one of her banshees possess the body of Blackthorn and integrated his soldiers into her undead army.
Blood elven Farstriders
The high elves originally founded the Farstriders organization as an adjunct to the general army, with a focus mostly on using information and specialized tactics to protect their kingdom from enemies. They never thought of themselves as rogues or assassins so much, however, since as followers of the Light, they believed that sort of thing was morally beneath them. The Scourge attack on Quel'Thalas changed much of that, however.
Having become the "blood elves" and thoroughly reworked their value system, the Farstriders decided that some degree of underhanded dealings was necessary to ensure their survival. They still remain one of the more high-minded elements in blood elf society however, and disapprove of many of the excesses that have been perpetrated by the Blood Knights.
Incidentally, the second most famous rogue protagonist in Warcraft is a blood elf, and a woman too: Valeera Sanguinar from the World of Warcraft comic. Her background story is an excellent example of what a typical blood elf rogue's story might be like, and integrates well with their history. She has little to do with the Farstriders, however; she started out as a homeless orphan who stole things just to get by until she was caught, sold as a slave in an underground Arena circuit, and trained to use her talents in battle.
Many players know Valeera by name and face, but few enough have actually read her story that a new roleplayer coming up short on ideas for his or her rogue could easily use her story as a kind of template many such characters might have faced in times of war. Just keep tweaking it until it's different enough from the original so as not to be plagiarism.
...have to wait until next week's article. Although this means giving rogues three whole articles in the roleplaying lore series, it seems only fitting that rogues steal more for themselves than any other class. For those of you who are just dying to feast your eyes on some awesome hunter lore and roleplaying ideas and simply cannot wait an extra week to read about them, check out Daniel's excellent article from Scattered Shots on how to design a hunter's character.
One final note on tauren rogues:
Most people say that there are no tauren rogues... but are there? Trust no one! The truth is out there! I want to believe!