The Tholian as depicted in ST-E was one of my favorites- not only non-humanoid but based on crystal as well.
I think the basic human form is fairly functional but it is not the only solution. Tripodal biology would be another one, and not the Species 8472 cop out where you just add a third leg to a biped either.
Trek over used the bump forehead aliens to the point is not a standard joke, but when most of the series was filmed the CGI and options were to expensive. I love B-5 and Farscape's Aliens, but even those could not deliver the performance an actor can with the eyes exposed. Even today that is hard to do, most are background characters (NuTrek) or still come across as overly textured and 'not there' (JarJar, young Yoda)
If there is another Trek series I think they could do a lot more in making aliens have a non-human structure and still be dynamic characters which can deliver a good performance.