Not Simulacrum. It used this spell.
Ice Assassin – Spell – D&D Tools
I'll pull out the relevant parts.
"An ice assassin spell creates a living, breathing creature that is a near-perfect duplicate of an existing creature."
"The ice assassin possesses all the skills, abilities, and memories possessed by the original"
"The ice assassin is under your absolute command."
So it targets a god, which in 3.5 were listed as creatures.
And from Pun-Pun
"Pun-Pun has the Ice Assassin spell as a spell-like ability at-will. He uses it to copy an arbitrarily high number of gods. Pun-Pun then commands a god clone to make him a proxy. This makes Pun-Pun a rank 1 demigod. Pun-Pun then makes another creature (Lokiyn, the originator of the trick, used squirrels) a proxy. This lowers Pun-Pun to divine rank 0. Pun-Pun then orders another ice assassin god to make him a proxy. At divine rank 1 again, Pun-Pun invests another squirrel with a divine rank. Pun-Pun repeats this process a NI number of times.
Then, he uses a standard action to recall each divine rank back from the squirrels. A NI number of squirrels with 1 divine rank invested equals a NI number of divine ranks recalled and gained by Pun-Pun. This gives Pun-Pun a NI divine rank.
Since Salient Divine Abilities are based on divine rank, Pun-Pun has a NI number of salient divine abilities. (That is at least all of the ones in the book and includes the awesome Alter Reality.)"
The problem is that 9th level spells, even Wish, can't make something or someone a god. It's not that powerful.