For QF domestic Y flights, I havn't found a website cheaper than qantas's. I normally only buy SS/Red, so if you want Full Y, maybe things are different.
For QF domestic J Flights, often FlightCentre have a few $$$'s off the QF price.
For International, I havn't found too much discount - about the best tip I have is to look for a Qantas website at the destination side and see if you can book your return trip there. Sometimes it's cheaper (eg Aus->NZ is often more expensive than NZ->Aus - so book your Aus->NZ tix thru qantas AU site, and your NZ->Aus return journey through the NZ one...)
You might want to investigate the AMEX QF card.
http://www.americanexpress.com/austr...rds/qantas.cgi
If you purchase more than $20K of QF flights over the year, you get between 2 and 5% back. Does not include Red tickets though, and the rebate is only for domestic travel (not int) although int adds towards the qualifying amount.
The margins for domestic tickets is negligible for travel agents. I'd be suprised if you found a TA that gave you decent discounts.
Another option is Qantas's Corporate sales arm:
http://www.q2b.com.au/
I know very little about them or whether you're even eligible to buy through them. Apparently you might get some QF rebates if you spend enough through them.
Good Luck !!