So, as the Explorers have been adventuring, they've been picking up NPCs along with them as they go. What is interesting, particularly in a campaign of this type, is that NPCs stick around. Usually, in campaigns I've run, an NPC might come and go. Perhaps they meet with the party and then go their separate way. In such cases, I've had NPCs disappear forever. Basically, the party just never does anything to warrant another meeting with that character.
However, in Rogue Trader, the Explorers have such a large ship that it's easy to incorporate particular NPCs into the crew. And once on the ship, NPCs can continually meet with the PCs. Thus, you can have a growing cast of non-player characters who grow and develop alongside the PCs.
Obviously, if you do this, you want to avoid video game type characters who sit in their room waiting for someone to talk to them. To avoid this, I wrote up a background for each NPC on the ship and then also wrote down one or two adventure hooks and personal goals for them. So if the PCs haven't really heard from a particular NPC for a while, I can just look up one of their adventure hooks or personal goals. Then, the NPC can actually approach the player characters. "Say, Lord Rogue Trader? I have a favor to ask of you...." From there, the resolution or non-resolution of the NPCs personal goal or quest can cause the relationship of the non-player character with the rest of the party to grow and change. Also, by keeping NPC goals in mind, I can have them react to things. "Captain! I must object to this course of action!"
One thing that I made sure of - I made each of their hooks and goals very short and quick. That way, I can glance at my NPC fact sheet and remind myself what it was that they have hidden in their past. I also made sure to only give them one or two. If I need an NPC to have more hooks, I can do that at any time. However, at the beginning of a campaign, I feel that it's a waste to put a lot of effort into developing random hooks that may go nowhere.
I've not had a chance to have one of my NPCs initiate something, mainly because the Explorers are currently busy with their own agenda. But I plan on this being a fairly regular thing once we hit the middle part of the campaign. All that said, in the latest session, two of my major non-player characters' goals came up. More on that later.
A Few Things - Good NPCs
Generally speaking, I've found that a good NPC has to be a really good supporting actor on stage. Meaning, they have to make an impression really fast, and then leave very quickly, so that the main characters (in this case the PCs) can do most of the talking.
Thus, it's helpful for NPCs to have little shticks or little hooks that can really convey who they are and what they are about in less than a minute. One good way to do this is to have a really distinct voice or accent for a character. A great example of this would be Demidov from the Dark Heresy episodes of the Minions of the Monster Podcast. With just a little accent and a few personality traits, Duck Sauce (the GM in those games) was able to make an NPC that the players really latched onto.
Unfortunately, I don't do voices nearly as often as I used to - mainly because I don't have the time to craft voices like I did in the past - but I've found that one doesn't need to be an expert impressionist to do a good character voice. A great example is Chris Perkins of D&D fame. If you watch this video podcast of Chris Perkins gaming with the creative team for Robot Chicken, you'll see that Chris does voices, but he doesn't have to make his own voice dramatically different. Just a slight alteration is enough to get the point across. In my opinion, this is a great example of how affecting a voice doesn't mean that you have to make an idiot out of yourself.
As I mentioned above, I've also found that helps me is to keep an NPCs goals and motives at the forefront in my mind. This helps them come to life whenever the game is running. For example, if I have an NPC whose mother disappeared on the plant of Sinophia and the PCs' space ship is going to pass by there, then that NPC should actually go and petition the PCs for a detour. And if the PCs don't stop by the planet, then perhaps he steals a shuttle and goes anyway. By keeping an NPCs ultimate goals in mind, it allows me to make living, breathing characters who do stuff when the PCs are not around.
Finally, I've noticed that people tend to remember intriguing characters and that they leave an impression most of the time. And one of the best ways to make an intriguing character is to give a character contradictory personality traits. Perhaps they're greedy, but have a soft spot for kids. Perhaps they're a stone-cold killer, but happen to be a really good chef and have the PCs over for dinner all of the time. If the tension is interesting enough, just having two contradictory traits can make for a character that will be remembered for a long while.
Another way to make characters memorable is to give them something a little more complicated than an adventure hook. Basically, give them an "unsolvable" problem. For example, a character might be a straight up coward in a gun battle. Or another character might have love problems. The only thing is that if you give an NPC one of these sorts of issues, you need to make sure that they're still things that party will care about.
If your NPC is a love-sick puppy, it's just as likely that the party will roll their eyes and not give his problems a second thought. If he's a coward, the party might leave him behind or expel him from the group. The trick is to make the NPCs problems matter to the party. For example, what if the ship's pilot has love-problem and it's affecting his performance on the ship? What if the colonial marines commander is a sadist and it's affecting the morale of the crew? By having an NPCs problem affect the PCs directly or indirectly, you give the player characters motivation for its resolution. The best part about these types of problems is that they can have long-lasting and far-reaching ripples throughout a campaign.