You must have been living under a rock if you never used a Palm Pilot with its associated "apps."
Here's a link to a March 2002 review of the Treo 180, where you will find terms like "SMS app", "apps list", "core apps," and just "apps".
http://the-gadgeteer.com/2002/03/12/handspring_treo_180_review/
The term has not only been used for a long time to as a shortcut for "applications," but it was specifically used to denote the little programs you run on a PDA, or even on Smartphones (to the extent a circa 2002 treo counts as a smartphone).
to be fair, you are arguing the wrong point. they didn't trademark "app" but only "app store."
it doesn't matter that people may have referred to their applications, programs, and/or tampon applicator sticks as "apps" before the app store. all that matters is that Apple brought the term "app store" into the public conscious. a judge doesn't care how generic a term is so long as it has acquired sufficient secondary meaning.