Bouncing in to revive an old thread here

As a gen-shipper, one of my favourite episodes for these two is Harbinger - I just love that Trip is defending Malcolm to Cole (that's her name, right? I think so, but that's also my dog's name, so I could just be confused

) and he won't let her slag him off. I do wish they'd foregrounded Trip and Malcolm's friendship more throughout the series, but I do love that it was always there, and always solid, and little moments like really made it. They're often characterised in fic as two people who bicker a lot, and while they do have their moments, there are just as many instances in canon of them being supportive and considerate to each other as there are of them bickering. I love the mutual "drop it" exchange here too.
Singularity is another huge favourite, just to completely go back on what I just said about the bickering - I think they just bounce off each other really well in that ep, and it just illustrates chemistry both the actors and the characters have.
I also love Silent Enemy, even though it's kind of pre-friendship, they're really starting to learn to trust each other and work together there and it's great to see.