What does the crew of a long range miltary aircraft eat during a mission?
It's not just the big bombers flying long missions; you'd be surprised how many of the sorties flying over Afghanistan, Iraq, Syria, Libya etc originate from airbases in Northern Europe with refueling stops over the Mediterranean (because closer airbases aren't available or are congested with aircraft from other forces or that have shorter ranges).

The short and simple answer is, aircraft crews eat whatever they can bring with them, that won't make a huge mess in the process. A bigger plane like a B-52 has some room to get up and move, so the pilot may take 15 minutes during ingress or egress, duck out to the entryway and eat a box lunch, then come back and relieve the co-pilot so he can do the same thing. Radar, nav and weapons systems officers typically have a little room behind or between seats to step away and eat, or they'll duck into the entryway as well. 

In smaller aircraft, space is more limited, but the pilot's flight suit will still have plenty of pockets to carry food and drink pouches. There are some considerations as to the exact type of food, especially in one- and two-seat jets. A crewman has to prevent "foreign object damage" to the switches and displays in his cockpit, or else his crew chief (and his CO) will be all over him about it. Good choices include pre-wrapped bar-type snacks; granola, protein, energy, some types of candy bars, whatever. Depending on what's available in the mess hall, pilots may be able to assemble simple tortilla wraps with lunch meats and cheese, which are edible with one hand and fewer crumbs than a bread sandwich. Anything that can be put in a drink pouch, like broth or tomato soup, is also a possibility. Bad choices include things like trail mix, peanuts, M&amp;Ms etc, as well as anything too loose to reliably keep together with one hand.

The bigger concern is, what to do when it comes back out? The B-52 has a rudimentary "head", with what amounts to a camping toilet (a bucket with a plastic bag liner and a toilet seat over the top) called the "honeypot". However, if it's used, the crewman who used it is often tasked by the crew chief with cleaning it, so it's considered a last resort. Crew of smaller aircraft have no such luxury, and unlike NASA astronauts, they wouldn't be caught dead wearing a diaper. Most fighter pilots eat a "low-residue" meal for the two or three meals before a very long mission or ferry flight, to reduce the chance they'll have to BM during the flight (some take an anti-diarrheal like Immodium as a preventive measure). Urination is a little easier to deal with, for men at least; pilots carry packets with an absorbent powder (not unlike what's in diapers) called "piddle packets". The difficulty is typically in... "maneuvering". You have to get the equipment out of your flight suit, when you're strapped down to the point of suffocation in a 6-point harness, then be able to aim into the piddle pack. Finally, you have to store this bag of piss somewhere until you get back to base, and as Rhino Driver is fond of explaining, if that base is a carrier, you have to make sure it's extra-secure, or on capture it'll go zooming forward toward the firewall and explode in a shower of damp absorbent crystals. Even if your squadron-mates don't see you getting out of the plane covered in this stuff, your crew chief will be sure to tell them all about it.