If I have already played an Australian copy of a PS3 game and then play...

... a US version, does that mean it will have two trophy lists, i.e. seperate from each other?

The question should still work for any other region.

It actually depends on the game. Demon's Souls has three sets of trophy lists for the US, UK/AUS and English/Chinese versions. I believe the same applies to Catherine and 3D Dot Game Heroes. Sega Mega Drive Collection and Sega Genesis Collection have two seperate lists too. That's all I'm aware of off the top of my head. Best place to check would be here http://www.ps3trophies.org/games/retail/

get the achievements.

I have an Australian copy of Grand Theft Auto 4. So I will have to play that and then the standard U.S.A version. I just bought it because of the Grey case which is better then our horrid Red greatest hit cases. I just borrow a regular copy. and find out