I'll second Keimbeggra, the eastern half of Bolivia is definately worth some time and totally different to the highlands, gives you a real feel for how diverse the country is. Not sure why it gets relatively little attention, its quite a wealthy region compared to the highlands and (maybe as a result) not much effort has been focussed on promoting it tourism wise.
The Missions are beautiful, how many you decide to see depends on how into churches you are. The first 2, San Javier and Concepcion (where theres also a museum) will give you a good feel and are fairly easy to access; San Ignacio a bit further on is also a bit of a transport hub for trips further afield (the church here has been completely rebuilt). There's also some nice countryside near them you could explore or do day hikes in.
Noel Kempff is superb but hard to get to. Last year (Sept/Oct) there was one bus a week from Santa Cruz leaving Thurs night that went past the turn for La Florida (called La Mechita) en route to Piso Firme and at least one other service from San Ignacio. From La Mechita you'd have to arrange for a vehicle to come in from La Florida to meet you. If theres a few of you you could hire a 4WD in San Ignacio. The northern side of the Park at Flor de Oro is excellent but access is pretty much limited to chartering a light aircraft so beyond most peoples budgets. All visits have to be coordinated via the SERNAP (Nat Park Admin office) in Santa Cruz who are helpful with details and also up to date info on access and conditions. Going with a tour will make organisation easier but wont come cheap and tours seem to really rush the Park (you could easily spend 2 weeks inside).
Other options closer to Santa Cruz are Samaipata and Amboro Nat Park, also the Chapare region. For other ideas on places the best Ive seen are the photos in books by Willy Kenning, a Bolivian photographer based in Santa Cruz. Browsing through some of his books (which are in most bookshops) will give you far more ideas than any travel guide Ive seen!
Have fun!
Images to inspire you.......