All these provide spectacular viewpoints and they are not far apart so that a very enjoyable drive can encompass them all.
A must see is 'Region des Lacs' consisting of around 9 lakes of crystal blue water. Here motor-powered boats are prohibited and fishing regulated. It runs from Clairvaux-les-lacs, to Doucier Via Les Frasnois and the Cascades du Herisson. The lakes are a haven for locals on a hot weekend in June/July and a great place for a barbecue or picnic, water tempertaures are usually around 20deg (depending on the time of year) and make for a very refreshing dip after a long hike.
The cascades (waterfalls), are a must see, while somewhat difficult in winter when the walking tracks can be frosty and slippery, it is a nature lovers heaven. Falls vary in volume of water with the rain, but range from 60m high to almost flat rapid filled rivers full of both wild and introduced trout, along the way you pass the ruins of ancient mills, which used the rivers constant flow to produce flour and other goods.
At the top of the Cascades du Herisson, is 'la Fromagerie' meaning cheese factory, there is no cheese factory here, however I believe there are plans to open a small store selling cheese from the region. here you will find free parking, (rather that the 5euro fee at the bottom), a wooden souviner store specialising in porducts from the area and a Friendly bar/coffee shop run by a young French/Australian couple with local dishes available. (if you ask nicely they will give you their WiFi Code.)They host concerts on the occasional weekend.
Le vache qui Rie" (the laughing cow) was founded in Lons le Saunier, the capital of Jura, and has an interactive museum open to the public for those who are fond of the world famous Cheese.
Accomodation in this area consists of guesthouses and 'campings', however if you are travelling with a tent you can pitch it almost anywhere without concerning the locals (obviously discretion is to be taken) there are facilities for camper vans all over France and can be parked/slept in in most public parking areas.
High End: 'Le Eoilenne' - Le frasnois, (top of Cascades Du herisson) mains average 25 Euro,Beers from 4euro 250ml coming back after a period of 'distaste' among tourists and locals alike. Not the place for a quick eat, but a good place for the yes sir no sir of a traditional Jurassien restaurant.