I play with different educational manipulatives for a living. (Visit www.weirdrichard.com and www.edventures.com). Over the past two years, I have constructed many fischertechnik models that require rivets. Many many rivets!
The fischertechnik rivets I use the most are the Single Rivet 4 (S-Riegel 4, #36323) and the Single Rivet 6 (S-Riegel 6 #36324). The Single River 4 is twelve mm in length (the pinning barrel is four mm long), and is used to pin two elements together. The Single Rivet 6 is sixteen mm in length (the pinning barrel is six mm long), and can be used to pin three elements together.
Step 1: Rivet Holder (Riegelschlussel #35799)
Rivet Holders are available in certain kits available from a fischertechnik retailer, and can be purchased as a spare part from www.fischertechnik.com. They also come up for sale on ebay.