Well, don't miss Foz do Iguacu of course....
but other than that (I've only traveled along the western side):
Bonito - 21.27.47S / 56.28.47W - just south of the Gran Pantonal. It is a place in the hilly jungle where a mineral river (chrystal clear) flows thru caves where you can scuba and snorkel among thousands of fish. You can also raft down it. Great accomodation and very reasonable at every level including hostels or camping.
The Gran Pantonal itself - famous swamp/grasslands teeming with wildlife. South entrance: 19.13.47S / 57.25.26W
North entrance: 16.14.33S / 56.37.20W
Rio Verde (Mato Grosso do Sul) - 18.56.16S / 54-54-07W - 'Sete Quedas' hotel and campground. It is right beside a series of 7 waterfalls and pools. Amazing!
Cuiaba is a very cool laid back city in the jungle and there are a few interesting places just a few hours north that you could do day trips to.
Enjoy Brazil! It's a bit expensive, but the food and people are great!