I like the direction IMPLIED by the Runemaster PrC: they grant abilities that any PC might want to take regardless of class. That said, there can be some PrCs more suitable for spellcasters and some more suitable for martials, and there can be PrCs that require spell slots to function, but those could just give +1 progression so that even a fighter multiclassing into the PrC gets a couple of spell slots.
I think all of these examples could work:
Incantatrix: grants metamagic, a handful of unique spells, some advantage in counterspelling/dispelling
Specialty Priest/Chosen of X: grants channel divinity, unique uses for channel divinity, divine luck
Artificer: accelerates item creation, enhance spell-like effects from magic items
Dragonmark Heir: enhance the dragonmark you took as a feat
Witch/Demon Hunter: grants resistance to spells and immunity to curses, see through disguises, special effect with critical hit on magic-using opponents
But to answer directly the original question: are there any that I miss? The answer is no. There were some well-designed ones, and some very flavorful ones, but I rarely saw any in play.