So this is what hit me first. Using Imperial Guard to represent a Rogue Trader household. Some of the most powerful RT dynasties would definately have personal militias.
It should be a smaller elite force, eclectic in style, with very little to no armour to speak of. Imperial Skimmers/Flyers should be the only vehicles present really, as an RT will be deploying from his ship. If he does have armour, it will be in the form of the most common of imperial tanks (Chimeras, Hellhound, Leman Russ Battle Tank) and thats about it.
HQ: Company Commanders are obviously the RT. The squad he is with could either be household guards, or family. Take Body Guards and maybe a fleet officer or master astropath advisor to fit the theme. Straken also makes a good RT, with his bionic enhancements that a man like an RT could afford. To model the RT, I would go with the Which Hunter Inquistors, Classic IG Characters, A Vostroyen or something from Necromunda.
Every RT with a private militia also probably has a head of that militia, or if he is the head at least a experienced 2nd in command. A Commissar Lord does very nicely in this role rules wise, as far as model goes, I'd say DON'T use a commissar model, but rather an officer from whatever you are using as your household troopers.
A primaris psyker may be pushing the edges of the envelope, as any RT with one is most likely stepping outside the boands of Imperial Law (more so that usual) and would likely draw the attention of the Ordos (esp Hereticus), which no RT wants. BUT There are those that will do it, OR if they are on an Inq sanctioned explorator mission, it maybe very likely.
Enginseers are also a decent fit. And chances are they will have a good amount of sevitors with them, as the RT will spare no expenses on having the best equipment.
TROOPS: Choices are Veterans to represent household militia. A Rogue Trader is going to have a small number of elite troops, rather than platoon sized enitites. Transports would be best represented via arvus lighters/aquila landers IMO, but Chimeras and Valkyries are fine as well, as some RTs are that powerful. Cadians work just fine as models, but so do Necromunda Enforcers or VanSaar, FW Elysians. Vostroyan first born will look particularly nice as well, as they are very ornamental
Penal Legion Troopers are also a good fit as mercenaries in the force. A fun unit for a themed army like this and a great opportunity for modeling unique a flavourful individuals in a squad.
ELITES: Storm Troopers are a good fit as the most elite of the household militia. I would go with old school ones over Kasrkin models. Just a more RT look to them. You can also convert up some fancier versions of your household troops, or a new look altoghter.
Abhumans are actually GREAT fits for RT armies. Ogryns and Ratlings would be easily aquired (via legal and illegal means) during a RTs adventures, and chances are that the RT has no scrupples over employing such deviations from humanity, after all chances are he/she deals with Xenos time to time. I personally think Ogryns are a better fit, but it is up to you.
I say psyker battle squads are out. To much psychic for an RT to afford/risk. That would definately bring down the Inquisition on them.
FAST ATTACK: If you take FA, stick with Valkyries and Vendettas. Maybe, MAYBE a hellhound or Rough Riders, but these are unlikely. Rough Riders though are eclectic, so maybe an RT would take them. BUT I would go with Vlaks still, as Heavy Support is going to be light.
Sentinels can be used to, but not armoured ones. If anything FW lifter sentinels make more sense, but a RT maybe able to convert them back in forth as needed, so guns can be found on them.
HEAVY SUPPORT: There is really nothing in the HS section that makes much since. If you aren't afraid of using FW models/rules, Vulture Gunships work. But a RT is unlikely to have tanks. If he does, it will be Leman Russ, and thats about it.
Modelling- Pick a consitent theme and go with it. Say you want to have fluff of a guy on the eastern fringe. Incorporate tau looking stuff into everything, maybe have a squad of kroot walking around (Penal Legion Troopers IMO). Want them to be fancy. Use Marcharius as your RT and then Vostroyans as all your troopers. High Tech, a Witch Hunter Inq in Power armour and Necromunda VanSaar/Enforcers as your troopers, along with Stormtroopers. Gothic, Witch Hunter guy in trench coat and Empire Soldiers kitbashed with guardsmen. Does he deal with eldar alot? Well use some eldar/dark eldar bits.
Then add little jewels of flare and ecleticism. Things like Penal Legion "Mercenaries" and Ogryns. Make these guys feel entirely different from everything else. Maybe use ogre kingdom ogres and make your mercenaries look like they are mongols as well. Maybe make them all look individual and criminal like. Maybe if you have a gothic force, make them look high tech and proffessional. But have a contrasting unit will go a long way to making the force fit the RT Theme
OR you can go completely inxonsistent and make every squad different to represent a totally eclectic RT.
What would be really cool would to see an actual codex on RT, or at least a white dwarf one. I am sure it would be very upgrade and wargear oriented and be designed aroung synergentic builds.