Technically, KotOR 2 has Visas Marr, who's probably the runner-up for Best Avellone Trolling the Player. That seems to be a thing with Chris.
In what way?
Visas truly loves the (Male)Exile, it makes sense, seeing as they experienced firsthand the destruction of entire planets(Malachor V and Katarr, respectively).
You tend to sympathise with others who went through the same hardships as you.
Oh, it's been a long time now. I just remember the way Kreia challenges the Exile on sniffing around Visas and "wanting to see what's under those robes" or something like that. Makes perfect sense in-character, even hints at a more intimately bitter side to the old hag, but even as a teenager I could read between those lines for Avellone's "got you, fucker!"
Truth be told, Visas has one of the - if not
the - most intimate scenes any companion had with a PC
ever in history of companions in cRPGs.
As for the subject:
P:T - an obvious one, but I think it should be noted that making a cast of memorable weirdos is comparatively easy; P:T I believe hits this sweet spot where said weirdos are also well written and likeable (unlike, say, Numanuma which operates on the same premise)
KotOR2 - another Cpt. Obvious; though I would like to admit that as years go by I think of Kreia as way too tryhardy more and more
Anachronox - it wasn't mentioned by now
how...? I don't want to spoil too much but Anachronox boasts some of the most creative companion designs ever
MotB - don't know what to say here, a classic
Mass Effect - I'll be honest, I think that ME companions are either BW's peak or close to it; some of the cast members are surprisingly nuanced, Garrus especially, and it's not at all in your face; and when it's in your face then ME can do it excellently - Mordin in ME2 is a prime example
Shadowrun: Hong Kong - honestly, I think that S:HK is one of the best examples of very standard companions done right
(an honorable mention) Disco Elysium - Kim Kitsuragi is finest, both of his precinct and in general