I like to put goblins at the top of the goblinoid social hierarchy.
In an upcoming campaign, kobolds are the ur-scalykin: all that slithers and snaps is spawned from them. Kobolds are not as powerful as the dragons, lizardfolk, yuan-ti, etc, but they possess far greater knowledge of What Is, and are generally much more insane for it.
I've run ghouls as a form of hivemind-like psychic/psychotic disease, all ultimately enthralled to the "Grey Mother".
Also in an upcoming campaign, phantom fungus is now an Outsider rather than a Plant, low-intelligence explorers sent out to fetch "samples" for their twisted extraplanar masters. (Gave them a gaze attack, too, to surprise those pesky adventurers with see invisible.)
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Also once ran a campaign wherein many the "cross-breed" monsters (eg, anthropomorphs, taurics, monstrous humanoids, mythicals, etc) were mostly beefed up relative to the standard versions, described as particularly gruesome mergers of creatures, and (mostly) made into insane Uniques-- the results of a corrupting aura from a fallen star fragment.