Donkey Kong Jr doesn't crash for me on startup like Donkey Kong and some others I've tried, and it doesn't complain about aeroplane mode either. The only crash I could get was if I said yes to uploading a new high score. Still, I took a look at it, and did the first patch for it. The code has changed enough that I haven't yet found a patch to disable the popup asking to upload a new high score, but this patch stops it from crashing if you say yes (it just asks again until you say no), and maybe it'll help with any other problems you're having with it that I'm not. I might have another look for the second patch another time, and will check the other games too.
It's for v65536 of the game, unzip & put DonkeyKongJrNoNet folder into /atmosphere/exefs_patches.