Top End sights

If you are driving up, I think you will need at least a stopover in Alice. It's a fair drive to Coober Pedy, then Alice, before heading further north.
Daly Waters is a unique place to call into for a beer and has an adjacent camping ground if you choose to stop overnight.
Mataranka is another place to stay for a day or two, either on the way up, or on the return journey. A great spot to chill out awhile in the springs, or the camping ground.
Katherine Gorge is worth a look see, so at least a one night stopover there and preferably two if you take a gorge cruise. (and swim at the waterfall)
On our trip to the Top End, we veered to the right and entered Kakadu National Park from the south, then exited from the west back to Darwin. Plenty things to see and do in Darwin.
Also Litchfield National Park is worth a visit, to the south west of Darwin, perhaps on the way back down.
There are many other places to see and experience, and I'm sure other traveler's and locals will give you more "must see" locations as well.

Hi jd

Have a look through My Blogs from 2009. We didn't see it all but we spent some weeks in the area seeing wonderful and amazing places. You are welcome to ask further about anything that appeals.

Motherhen

take some pool noodles to be able to enjoy floating down steam at Bitter Springs in Mataranka. :)

Jd,

If in Darwin for a few days, check out the aircraft museum. Also, when you're hungry at night, go to Stokes Hill wharf, for a different dining experience.

Mindel Beach markets are worth a look too. Think they're on Sunday and Thursday evenings.

Bob.