Just in case there are people here who don't know about the Serges-Wily theory, a little bit of information. This is from the Japanese script, so disregard the localization.
-Serges' designer said that he used a "certain mad scientist" as a template.
-Serges refers to X as "Rockman X", when only very specific people like Dr. Cain refer to him as Rockman X.
-During the audio transmission from the X-Hunters to the Hunter Base, Serges momentarily refers to X as "Rock".
-When defeated a second time, Serges very specifically says
"Am I to perish here? Defeated by Light’s memento robot again… regretful…". He is the only other character in the series to mention Dr. Light's name, and the way he mentions it, it seems they knew each other. Serges says that he was "defeated by Light's robot AGAIN". This is probably the biggest hint and the greatest confirmation. Note that he doesn't even say "Dr. Light", just "Light", like Wily would say.
-After being defeated, Sigma claims that Zero is "the last of Wi... Num...." which obviously means "Wily Numbers", as in robots created by Dr. Wily. How did Sigma gain such knowledge of the past? Well, he most definitely had Serges to thank for that...
-X2 is the first game where the boss refights happen in teleportation capsules, just like the ones Wily used back in the day. Coincidence? I don't think so.
Wait, were all of the Sigma bodies pre-built? I always thought that they ended up being built by Mavericks or kind of just... built themselves somehow.
Fuck. I love these games.
Depends on the game. Sigma's body in X2, while no official confirmation was offered, was most definitely built by the X-Hunters or Serges himself.
On X3, his body was built by Doppler.
On X4? Who knows. Pre-built? Wily?
On X5 his new bodies were built by Wily.
On X6 he was being repaired/rebuilt by either Isoc or Gate.
X7? Only god knows.
X8? Again, who knows. Maybe Lumines?