The things I most often sent were:
~socks
~gel insoles
~chapstick
~eye drops
~nuts and sunflower seeds
~trail mix
~jerky
~tuna pouches
~dried fruits
~olives and pickles (DH loves them as a snack...lol)
~peanut butter
~plastic bottles of jelly
~books
~movies
~video games (DH took a DS with him and his roomie had a PS2)
~specific toiletries (the things DH couldn't find at the PX)
~pictures in little frames - like the wallet sized ones
~drawings from the kids
I would recommend seeing what he requests once he gets to his base. For instance, during DH's second deployment he was about as far as he could possibly get from the DFAC, so he really appreciated packs of tuna and boxes of crackers for the nights he just didn't feel like walking down there. Also find out if there are any unit specific things that he cannot have - this last deployment DH wasn't allowed flash drives for anything while my friend's DH's unit had no problem with them. Check to find out what he's got easily accessible to him - one time DH had a microwave and one time he did not.
I liked to do themed packages too - Christmas box with miniature decorations, Cinco de Mayo box (tortillas, refried beans, velveeta, salsa, chips, non alcoholic margarita mix, decorations from the kids), etc. It was really fun coming up with ideas. I think I did one themed package a month and one regular package, plus anything else he asked for. One thing that helped me was to take a walk down every aisle at the grocery and look specifically for small things packaged in non breakable packaging. That's how I found green olives in a pouch - I would have never thought to look for them but they are one of DH's favorite snacks and he was very happy to get them.
I definitely agree with ziplocks - put everything in a separate ziplock. It will help protect against damage and the guys can almost always use ziplocks. For baked goods, stick a slice of plain white bread into the container with the cookies/brownies/whatever and it will help to keep them moist.
While I was typing this I was asking my DH what he liked in his packages....he named off a few things but then said that it really didn't matter to most of the guys what was in them, it was just that they got something at mail call. On that note, send lots of random "I Love You" cards too.

And remember that the guys do a lot of passing things around, so anything you send will get put to good use by someone.
My DH's favorite thing for me to make was German Chocolate Brownies. They are super moist so they were still moist by the time they made it over there. I'd be glad to share the recipe if it's something you're interested in.