Naturally, the moron that I am, I chose the wrong ones on my first playthrough! The choices I eschewed are, in both cases, way better than the ones I chose, from a story and character development perspective.
THE FIRST CHOICE: The Infestation of Haven
The Context: So in one of the early missions you save a bunch of refugees from a planet called Agria, who got in the way of the Zerg invasion. Dr. Ariel Hanson, who is in charge, joins on with you for a while while you drop them off on a refugee staging point called Meinhoff.
However, things get worse from there: at Meinhoff, it turns out that some refugees (maybe from Agria, maybe not) have been infested, and the zerg virus spreads quickly throughout the camps. Raynor has to come back and burn out the infestation, and take the surviving refugees away. Ariel finds an uncolonized planet they call Haven, and decide to land the refugees there. It's close to the edges of Protoss space, but hopefully should be safe enough.
It isn't. The Protoss show up, and their Observers detect Zerg biosigns on Haven. Some of the surviving colonists were infected, and now it's one again spreading. There's now a big Protoss fleet under the command of Executor Selendis hanging out in orbit, intending to purge the planet.
The Choice: Standard procedure indicates that Selendis is right: the only solution to a Zerg infestation is purification by fire. But Ariel is convinced that she can find a cure for the Zerg infestation virus is given just a little more time. You can either back Selendis' play and perform the purging yourself, razing infested sites and keeping it from spreading, or you can instead oppose Selendis and, as she puts it 'meet her in glorious combat'.
What I did: I opposed Selendis. I'd spent too much time on these people to abandon them now. Plus the way it was worded made it sound like if I backed Selendis' play I'd be killing every Terran on the surface, which is not actually the case.
After you shoot down her Mothership, Selendis acknowledges your skill and withdraws. Doctor Hanson manages to find the cure she was looking for, and Haven is saved. Ariel leaves the Hyperion at this point, but not before informing Raynor that he's a 'good man' and giving him a quick kiss.
Not a bad cutscene. Certainly made me feel good inside. But compared with the other thing...
What I could have done: Purify the Zerg infestation. This mission is actually a LOT harder than the other one, incidentally.
Ariel, understandably upset, locks herself in the lab while you do so. At the end of the mission, you're told that there's a Problem in the lab. We are then treated to a cutscene of Raynor, in full Marine gear, treading carefully into said lab.
Turns out that Ariel was, herself, infected, and her infestation is now 99.33% total. She's still able to speak but is otherwise mostly Zerg. Raynor, naturally, has to kill her, but what makes this option better is the brief conversation they have right before she pounces him:
"Will you enjoy killing me, Jim? Like you killed my children?"
"You're infested. You're already dead."
Why is that interesting? Because one of Jim Raynor's driving motivations is Kerrigan, a likewise infested human. That one sentence tells you exactly where his head is at with regards to Kerrigan: "You're infested. You're already dead."
THE SECOND CHOICE: Tosh or Nova
The Context: For a while, you're working with a shady fellow by the name of Gabriel Tosh. After a while, Dominion Ghost Nova (of the aborted Starcraft: Ghost spinoff game) shows up and informs you that Tosh was part of an experimental part of the Ghost program to create agents with strong psionic powers, called Spectres. She also informs you that every Spectre so far has gone on a psychotic killing spree, and that as such the Spectre program has been shut down. Tosh is planning on using the rare resources you've been harvesting for him to start up the program again.
The Choice: You can side with Nova, and help her take Tosh down and stop him from unleashing a bunch of murderous whackjobs into the sector. Or you can side with Tosh and help him break his fellow Spectres out of the Dominion prison. He'll stay on with you and help you, but again you've just released a bunch of dangerous people.
What I did: I sided with Nova. After you finish taking his facilities apart, he threatens you over comlink, and then a comic scene follows where he tries to kill Raynor with a voodoo doll - it doesn't do anything to Raynor, but it does seems to cause his buddy Tychus some trouble. Then Nova comes up behind him and shanks him.
What I could have done: Help Tosh bust his buddies out of New Folsom prison. Not only is this mission just straight-up more fun than Nova's, it means you can still get Tosh's commentary on various events.
In the cutscene afterwards, Tosh expresses gratitude, and swears that he and his Spectres are with you to the end: he wants Mengsk dead as much as you do. Raynor's second-in-command, Matt Horner, points out that they did more than just break out a bunch of killers: they also busted out all sort of artists, writers, and other political prisoners that Mengsk had had thrown into his gulag, and gets all idealistic on them. he says again that they're building a better future. And Raynor, sort of sadly, says that that better future they're making is great...but it's not for the likes of him and Tosh.
While the other cutscene is fun, this one, again, gives more insight into Raynor's character. He wants to take down Mengsk. But he's willing to make deals with the devil to do it. He's not a white knight on a horse, or at least he doesn't think of himself as one.