Darwin has a number of choices, but limited when it comes to chains:
IHG - Three properties all owned by the one owner, original HI is in the old travelodge shape (same as HI MEL), and is OK, HI next door is in need of a reno with poor mobile reception due to its design with most rooms having an ocean view , both HIs have good parking. The Crowne Plaza is the former Sheraton (and Rydges for a short time), has poor parking but cheap valet, nice rooms and an ice machine on most floors.
Novotel - Have not stayed there but average by reports.
Mantra - two properties, one on the esplanade and dated, another in middle of the CBD, both are OK.
Vibe/Medina - tried this property twice, never again, first time no towels, second time had a balcony but no door to access it, and parking is a joke with it being the only area in Darwin thats metered to 10PM every night, while paid hotel carpark is available, often there is a waiting list to get the access cards.
Quest - Number of properties throughout Darwin, being more apartment style good for longer stays.
Casino - new accommodation is great, and they have a very good wireless internet system now in place.
Rydges at the airport - I have only stayed at the resort which is dated, nice pool but limited dining options, and surprisingly very quiet despite Darwin having a lot if midnight flights.
There are other options that I have not used re accommodation, and I recommend booking early during the dry.
Other tips - get a cab into town on arrival if you get a PM flight, and grab the hire car from town next day (its an easy and quick walk to the offices of the majors), but dodge Hertz as they charge if you want drop it off at the airport on return, and also watch fuel levels on pickup, because its 100km per day limit, often the cars will show full but have already done a bit of driving on the tank, so I normally pick up and top up, taking the receipt with me when returning the car for a refund.
Another tip - dont go swimming in the harbour!
http://www.ntnews.com.au/article/2010/06/09/154301_ntnews.html