Fossdroid get the popularity data (most popular and trending tabs) through Piwik API mostly elaborating the pageviews and the downloads.
In this way it’s possible to list the top 10 best apps/games viewed on Fossdroid.com (last 6 months):
Download apks from Google Play Store
Block ads/hosts via DNS
Play YouTube videos
Lightweight YouTube frontend
Material Design CyanogenMod 12/12.1 theme
Upgrade your mobile device to a full-fledged tricorder
Simple solitaire klondike game
As you can see the Yalp Store wins the battle: it allows Android users to download apks from Play Store without OpenGapps/others (you should create a fake Gmail account because this app violates the Play Store ToS).
The statistics regarding the total number of app-downloads of F-Droid could be/are different because Piwik elaborates the data from fossdroid site and only F-Droid knows the real stats (this explain why F-Droid is not in the first position).