I took my JanSport pack to Ecuador a couple summers ago. I ended up getting a cloth laundry bag and stuffing the loaded pack inside to keep my straps from going everywhere. Granted, I was not packed for backpacking, so I didn't have my stove, pot, etc. that looks so crazy on x-ray.

My brother-in-law just joined the Peace Corps this spring and flew to the Republic of Georgia with a similar setup. It worked well for him, too -- but again, no stove, no pot, nothing suspicious looking.

The duffel mentioned above is a good idea, too. That idea gives you a bit more room to pack things like a post-trail change of clothes.