Pretty much variations on what others have listed with a couple additions. Sometimes I'll pick up some of the pre-packaged apple slices, and something that works surprisingly well, albeit they can be a little messy depending on how it's packed, is a good 'ol PBJ. My wife started making them for some rides, and I was surprised just how good they tasted when we stopped for a roadside picnic. A little can of Deviled meat and crackers or a couple slices of bread works too. Lots of snacks are available in 100 calorie packs and many things you can toss in a ziplock snack bag. My wife gets the boxes of snack sized beef jerky for me too, as well as the meat stick/cheese combos. Until not long ago, we were full-timing in our RV and traveling the US, so I always had a little bunch of snacks beside me while I drove. That experience pretty much refined our snack methods. Sure, we had a refrigerator and pantry with us at all times, but having ready-to-munch snacks within reach was nice.
Although I haven't used it yet, I recently picked up a collapsable cooler, that I keep in the top case, at an end of summer closeout sale at Target. For several years now I've ridden with a TAKAYA 24 vacuum bottle with a screw on lid that'll keep ice all day. Here in the desert southwest, I always have two bottles of water in the bike. One of those little drink flavor envelopes can give them taste and will keep a long time.
I was looking for a trunk organizer and came across a small back-of-the-seat organizer in Autozone for $10. It holds my two "emergency" water bottles and can hold snacks too. I screwed it to the back of the top box. The collapsable cooler is less for snacks than for quick trips to the grocery store. It stays in the trunk and can work for larger lunches. It's waterproof, and we keep a plastic half gallon milk bottle full of water (ice) in the freezer so that it's always ready to drop in the cooler. It wouldn't work for multi day rides unless we stay in a motel where I could re-freeze the bottle overnight.
Although we've always packed a lunch or snacks on rides, and usually put them in a little cooler with one of those blue ices to keep it cool, I tend to lean toward stuff that doesn't need to be refrigerated or doesn't need to be kept very cold. She likes to throw in something with chocolate, so that requires cool storage.
The cooler is only a couple inches high when collapsed, but it is quite roomy when expanded, and it still fits in the trunk at full height. The organizer is supposed to be waterproof too, although it isn't insulated. It velcros closed so doesn't take up much room in the trunk when not being used.
