The thing to remember is that there are two words for "application". Apple use "application" (with the suffix .app) on OS X. Microsoft uses "Programs" (suffix .exe). Application is linked with Apple, so when they call it the "App Store" it is based on their previous use. "Prog Store" would also not be generic.
It may have been answered already but Apple uses the suffix .ipa for iphone/pod touch apps whereas "Programs" to me is nowhere near ".exe" for which I thought stood for "executable." You know, I'm just sayin.