You should watch the whole show, it's not that long but it's really good.
Anyhow this got me thinking about what each ponies cutie mark would be:
Mal: This one's tricky a gun seems like a cheap way out although it would work.
Zoe: Once again a gun would work but also seems like a cheap way out.
Jayne: Bit easier to avoid the cheap gun here, you could give him something death related like a skull since he's more of a mercenary/thug than a soldier.
Wash: Easy, a pair of wings or similar flight symbolism.
Kaylee: Cogs or a spanner, something mechanical definitely.
Simon: Something doctory A cross or that twisty snake thing.
River: How do you encompass a natural ability at everything into a single symbol?
Inara: Another hard one possibly interconnected male female symbols?
Book: Seems like the problem here is giving him a mark which isn't an immediate spoiler. Something religious with the implication it's make-up hiding the real one?
My opinions on thus-
Mal: Captain's bars. He's captain of Serenity. I think he was a sergeant or something in the war, so sergeant stripes would work too, I suppose. Also Earth Pony.
Zoe: I think she was a corporal, so the appropriate insignia, which escapes me atm. Earth Pony.
Jayne: I don't think a gun would be inappropriate here at all, especially if said gun was Vera. Earth Pony.
Wash: Agreed. Wings would be excellent, or possibly a steering wheel. Pegasus, obviously.
Kaylee: Again, agreed. Earth Pony, maybe Unicorn, possibly.
Simon: Agreed once more. Unicorn here.
River: Perhaps a brain? Or an infinity symbol? I 'unno. Unicorn, definitely.
Inara: Agreed here as well. Once again, Unicorn.
Book: No real idea for the Cutie-Mark from me. Earth Pony again, methinks.