Set’s main cult center was Nbwt, the Greek Ombos, present day Naqada. It’s ancient name derives from the name for gold, This was due to to the towns proximity to the goldmines in the Eastern Desert.
Now a days it’s known for the Naqada culture, which is broken into 3 parts. Naqada I or Amaratian culture was a pre dynastic , Upper Egyptian Culture that lasted 4000-3500BCE. Naqada II is also know as the Gerzeh culture lasted from 3500-3200BCE. The last phase, Naqada III is also know as Dynasty 0 lasted from 3200- 3150 BCE.
In not as ancient times Naqada is the home to both the main temple of Set who was also had a temple at another Ombos known as Kom Ombo, also known as Nbwt. Though this second temple has more to do with Sobek.
Another cult site is Sepermeru,at this site the shrine of Set was called “The House of Set, Mighty is his Arm”. The site also hosted a separate, independent, temple to Nephthys.
There was a cult center in Avaris or Hawara, as well. It was a major administrative center for the Hyksos during their rule. This is one of the places were there is evidence of trade with the Minoans.
Many Oasis were also cult centers to Set. A small list of these include the Dakhla Oasis, the upper Egyptian town of Kellis, now known as al-Kharab, and the Kharga Oasis, one of the homelands of the Beja people..