Does working for a prestigious company help in a PhD application?
The short answer is "probably." The long answer is "it depends."

Admission to a graduate program is almost solely dependent on how well you impress that department's graduate admissions committee (assuming you meet any minimum admissions standards: grades, GRE, etc). If they attach value to your work in industry, it'll help you out immensely. If they don't, it probably won't hurt you.

This Kaplan page outlines the general process.