There isnt much out there to make a decent list of the top 5 guilds and have it not be the same as it was 2 months ago, or still be the same 2 months from now. Based on how the expansion has gone so far, I would vote for Second Dawn, Dissolution, NPU, Strike, and Chaotic Legion in no particular order, but thats all based on how familiar I got with each name by hearing what they had done first. To maintain a list, thats a little harder to do since there cant be much server to server competition.
However, I remember a man who liked to used Tiering as a way to rank stuff

so maybe Tiering off the guilds could be fun, have certain things that need to be slain in order to reach a tier.
Tier 1 could be killing all 8 avatars and the other EOF contested on top of Tier 2 stuff No guild would be here yet, but the first 5 could be the top 5

Tier 2 could be any 4 EOF contested on top of Tier 3
Tier 3 all instances and KOS contested
etc...probably a better way to do this, but not the point
or maybe a Raid Guild DKP system lol, guilds report in what they kill every week and are given points accordingly. Might be hard to keep track up but there could be a forum for that, similar to the progression list, but able to keep up with more than just first time killings.
Or instead there could be a server point battle for contested, most top guilds are dominant, but there could be a few slip ups that could cause them to lose a mob or 2. If it were just for EOF contested have say 50 points, 5 per mob and if the non-dominant server takes one, then that uber guild would only be a 45 till they can take it back, if they can. This could promote competiton for some servers, maybe not, seems like most servers have just 1 hunting avatars so this probably wouldnt be as exciting as I would hope it could be. KOS contested still go either way here, hopefully this increase in avatar frequency will push a few other guilds into the fray.