To begin with, the seat back pockets rarely get cleaned. Used napkins, chewed gum and the mucous covered hand of a previous passenger are all things that have likely been in that seat pocket since the last time it was cleaned. So here's what I do...

Everything I'll need to access during the flight goes into a plastic bag, including my computers, pens, NYTimes, USAToday and gum. The bag goes into the seat back pocket. If I need anything, only the inside of the bag gets touched. At the end of the flight, the bag comes out, everything in it goes in my computer bag and the plastic bag gets trashed. So long as everything goes in the bag, nothing gets left behind in the seat back pocket. And I've cut down my exposure to who knows what.