Going over the entire JMS run as well as the more current issues, I think JMS and crew don't get enough credit for creating new villains for Spider-Man to face. Even during "The Other" there were still 3 new villains being created or used at the time. Just to save some time I used some of Spiderfan.org information so thanks to them for it but here they are:
Name: Charlie "Vibranium Man" Weiderman
Powers: Covered in a mixture of vibranium and a porous breathable alloy, it gives him super strength, durability, and the ability to vibrate through the hardest of substances.
Appearance: Amazing Spider-Man #515-518
Name: Digger a.k.a Freddie Carnevale, Santo Castellani, Jimmy "Little Man" Desanti, Louis Fredone, Tony Mascapone, George Sims, and seven other unnamed mobsters
Powers: A collective consciousness of 13 dead mob bosses in one mixed with gamma radiation gives Digger superhuman strength and durability although deteriorated after exccess fatigue.
Appearance: Amazing Spider-Man #51-54
Powers: Flight, super strength, high durability, projectile poison.
Appearance: Amazing Spider-Man #46-48
Powers: Able to absorb totemistic energies thereby enhancing his strength, stamina, and speed. Also able to track down his prey no matter what the distance. A mix of Morbius the living vampire with Sebastion Shaw if you will.
Appearances: Amazing Spider-Man #30-35, 525-528, FNS #1-3, MK Spider-Man #19, 20, 22
I'll add in some of the bio's but there are a few more I'd like to post. These villains in particular are very cool in that Charlie and Digger were created by more scientific means while Morlun and Shathra were more mystical in origin. Next up, Grey Goblin, Sarah Stacy, Dr. Carlyle a.k.a Doc Ock imitator, Ezekiel, Tracer, Ms. Arrow.