To me, Picnic at Hanging Rock is easily our best. It was only after I came to that opinion that also I learnt it was responsible for resurrecting the Australian film industry from the dead, therefore making it one of the most important films in our history.
Our next best by my reckoning is Breaker Morant. It's like our version of Paths of Glory.
Daylight comes next, then a group of films I very much enjoy but can't be bothered ranking properly...
The Interview
Chopper
The Castle
Bad Boy Bubby
The Adventures of Priscilla, Queen of the Desert
Love Serenade
Mad Max
Mad Max 2
Romper Stomper
Two Hands
Proof
Strictly Ballroom
The Adventures of Barrie McKenzie
Walkabout (does it count? I think it was funded domestically. It feels very Australian nonetheless)
The work of Australian directors, such as Dark City by Alex Proyas, and Master and Commander, The Truman Show and Dead Poets Society by Peter Weir deserve a mention too.
EDIT: I was a bit taken aback by those slighting Blade Runner, but then I remembered I would've had similar words about it once upon a time. It's a movie that gets better and better everytime I see it. I now hold it in very high esteem, and i'd probably rank it in my top 3 Sci-Fi's of all time. And what other nigh 30 year old film has special effects that look as good as what we see in Blade Runner? Very, very few. That alone is a testament of Ridley Scott's work and vision.