If I were choosing for myself, I'd pick the crocodile, because I seek wisdom and they are a symbol of that, being such old creatures and such successful survivors.
Here's my current list for SGA1:
(note: I don't have picture hosting capability, so these links go through to various sites; I don't expect people to click on them all, I just want to give a sense of what I mean)
The Fox: skilled, cunning, swift, inquisitive, courageous, able to hide in plain sight. Also sleek, gorgeous and the colour of the saddest autumn.
The Snake, and I don't mean the ridiculous Christian snake-as-devil, I mean something more along the lines of the Wagyl (or Rainbow Serpent): a beautiful, sinuous emblem of wisdom, strength and sexuality.
A Seagull, because he has a soaring intellect, but is also noisy, inquisitive, confident and likes to squabble with everyone else, but he's also unexpectedly beautiful.
John is really hard, but I think I might go for something like a Lynx (secretive, dangerous, pointy-eared), or perhaps a Stingray (winged, elegant, dangerous, good at camouflage and manoeuvering into a strong tactical position). But I can also see arguments for things like a starfish, chameleon, grasshopper... or maybe a hawk. Hmmm. Maybe he should be a mythical creature, like a hippogryph.
But enough of me. What are the totem animals you'd choose for your favourite characters?