Depends on if you’re asking for all kanji or just the jouyou list. For beyond jouyou, it’s looking like コウ is probably the winner.
Edit: So I actually counted characters for the onyomi readings from the official Kanken dictionary, and the top 5, in order, are:
コウ (248字)
ショウ (229字)
ソウ (173字)
シ (162字)
カン (153字)
I think someone else counted from the 大漢和辞典 and コウ was still the most at over 2000 characters.
If that is the case, then how little words does wanikani have? According to Jisho, 987 words have the “jou” sound in them, and 1214 have the “kyou” sound in them.
In the grand scheme of the whole language? A tiny fraction. The latest edition of the Kojien dictionary has something like 250,000 entries. Even in comparison to the size of the average active and passive vocabularies of a native, it’s not going to be enough to have a fully-formed vocabulary. That’s why most people move on to something like Core 10k after WK or supplement with that while doing WK.
Hmm, ok. How do people find things like Core 10K? When I look up things to use to learn Japanese, things like that don’t tend to show up.
Yeah, this is my first time hearing of it too.
This thread may be helpful for you:
Ahh, there’s so many other Japanese learning tools I start hearing about daily
currently I only use WK and someone sent me some Genki PDFs but I don’t quite know how to use them properly, and I don’t know what else to be using 
only 27 x かい ? It feels like i come across this reading every single day that i do reviews… or maybe my leeches contain alotta かい…
Yeah, WK is only one piece of your learning journey. You’re going to need to also start building your grammar foundation. And while WK can be a good start for learning words to build your vocab, you’re going to need many more even beyond that. Even Core 10K is not going to be enough.
In that case, shot in the dark: What resources do you suggest at an early stage? I know absolutely nothing about grammar.
i try to use different meanings and memonics for different kou or shou or shin.
For free resources there’s Tae Kim, Cure Dolly or Imabi.
For textbooks I think most people use Genki or Minna no Nihongo.
When in doubt, こう!
Though しょう seems to be slightly more likely I saw in the post above =P
But こう FEELS more common 
When I don’t know the answer I just put E, to get to the info.
It is almost never right, until it was! I tried こう, was told “We want kun”… um… no. “e”… correct XD
SO the one time my “E for eeeeh I don’t know” was correct, I wanted to put こう, which WAS correct, just not their preferred reading =P
It was this one: 江 https://www.wanikani.com/kanji/江
Funny, cause a katakana エ looks like kanji for construction 工
Tip: If a kanji has the radical 工, the on’yomi will be こう 
Might be exceptions… but most of them are, by design =)
Highly recommend that script! <3
True but doesn’t often happen that the kun’yomi is also え at the same time.
True! え is a fairly rare one! Which is why I use it as my fail =^_^=
Hm, don’t remember what Kanji the katakana was derived from… Could be that one for all I know (since it has the shape and sound, which is sort of how they made them =P )
Edit: It was! =D
Simplified in the Heian period from the man’yōgana kanji 江 , taken from the right part of the character.
This maybe a bit overwhelming, but since you’ve asked:
pinned under Resources section.
A megathread is just what I was after, really. ありがとうございます
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