A gift for the son is nice but not necessary - depends on how close you are. I find boys a little more challenging to buy for a confirmation (since a nice bracelet or pendant doesn't seem to fit), so I usually do a savings bond. I've seen some nice plaques and frames that are appropriate, but you would probably need to go to a store that has specialty religious items. If you know his confirmation name (some religions permit the confirmant to choose a special name for the occasion), you could get something that highlights the name or explains its derivation/significance...
As for Dad, it depends how quickly he's shipping out. One idea is a gift certificate to a portrait place - they could have a family photo taken before he leaves so he has a nice one to take with him. If there's not much time (for the photo or the dinner out), what about one of those recordable story books? I know they seem more appropriate for little kids, but I think all ages appreciate hearing the voices of the ones they love...