My favourite places to stay are the Marriott and the Stamford. Both are on the river, and walking along the river at sunset time is just glorious. If it were me, I'd stay at the Samford, have a luxurious buffet breakfast overlooking the river in the morning, walk through the Botanic Gardens, and then across the Green bridge to Southbank. Wander through Southbank, check out GOMA (art gallery), see a show in the evening if something takes my fancy. You can also catch a CityCat during the day from Southbank and take a ride up and down the river just for some fun and sightseeing.
If you haven't done Brisbane before and had time I might also catch a bus up to the Mt Cootha lookout and plan to have either a meal or a coffee out there and take in the view.