In addition of the Blacksmith shop and the three first LEGO factory sets, the following sets have een designed by fans:
10190 — Market Street was designed by Erik Brok. Erik sadly passed away a few month later.
10183 — Hobby Train was designed by a team of 10 fans who created 30 different models, all of which are buildable with parts in the set. The fans were Ben Fleskes, Christopher Masi, Holger Matthes, James Mathis, Jeramy Spurgeon, Mike Walsh Cary, Pierre Normandin, Reinhard Beneke, Steve Barile and Tim Gould. All of them high-profile builders, and the set was nothing short of fantastic.
10191 — Star Justice, designed by Chris Giddens, against 10192 — Space Skulls, designed by Mark Sandlin. These sets had less success although the were very versatile and allowed for countless hours of space building.
10200 — Custom Cars Garage, designed by Joe Evangelista, Joe Meno and Stephan Sander, all well-known names in the LEGO community.
Also, you have to keep in mind that the line between high-profile AFOL and LEGO designer is becoming very thin, and some people have crossed that line (Pierre Normandin, for example). As such, can't it be said that the sets they design now are created by fans? Designers are fans in their own right!
Also, in addition of the fans-turned-designers, LEGO does invite fans for workshops from time to time. Theire influence on 10194 — Emerald Night, for instance, is obvious, if only for them pushing LEGO to make big train wheels.
So, the line is blurry, and that's for the better.