Admittedly the Padres history is not rich with famous September callups (is any team's?). The Padres callups history would be better served by recounting the most famous June callups (Dave Winfield, Jake Peavy, Kevin McReynolds, Chase Headley twice). The most historic callup in Padres history (Tony Gwynn) happened in July. However, when the question was posed to me one player immediately came to mind.
The 2003 season was the swan song for Qualcomm/Jack Murphy/San Diego Stadium as a baseball venue. In September of that year that song was reach its finale.
The Padres' lone All Star, Rondell White, was traded mid-season. Come September the best Padres fans could hope for was to see someone promising that would help usher in a new era in Padres history.
Enter Khalil Greene. Just over a year after getting drafted with the 13th overall pick in 1st round, the Padres called up the promising SS with the golden locks. His defense was flashy and impressive and his bat had promise. His actual September performance that year was not something to write home about, but at the time it was a symbol of a promising future and in hindsight he was a key piece to a run of 4 straight winning seasons (the longest such streak in franchise history) and two division titles. It very well could have been that experience in 2003 as a September callup that aided him in his good to great individual and team performances over those next 4 years.