16th November 2016: This might seem a bit random after such a long time, but I've just been through my old YGO Shipping Challenge journals and cleared out all the broken links. This means that a fair few pairings that weren't available before (either through being reserved by a deleted account or filled by a submission that's now no longer there) are available again.
There's still no separate lists for ZeXal or Arc-V, because I'm afraid I don't keep up with those series to know the shipping names, but please do feel free to submit fanwork for them as well if you want to and I'll gladly add lists for them as needed.
Also, I took out the rule about "no submitting older works" because, let's be honest, the challenge has been inactive for a long time now, so if if ever hopes to be completed at all then allowing older works might be the way to go. So feel free to go back through your older YGO fanwork and submit any ships for the challenge that still need filled. In fact, please do! It'd be nice to see this lonely challenge get some love again, haha.