Beneath a Steel Sky's Joey, Planescape: Torment's Morte and Primordia's Crispin are the best companions *ever*. They're not particularly likable or useful, aside some particular instances with each one, but they provide a stark contrast of lightheartedness and humour against otherwise post-apocalyptic serious dark backdrops and settings, bringing some humanity into the whole equation, and making the games they're in more relatable and in touch with emotional reality.

Now, on the opposite side of those, I'd have to say Dust: An Elysian Tail's Fidget... nothing more than Navi on steroids, pretty much the most annoying companion to ever grace a video game. Appalling voice acting, "cutesy-pukesy" design clearly made to please "young sensitive" gamers born on the internet age, who gladly swallow every single CUTE KAWAI ZOMG! FURRIES! thing people shove down their metaphorical throats, annoying interruptions, pseudo-funny jokes that only 6 year olds could probably laugh with... she's a mess. Fortunately, she is pretty useful in combat, but the rest is just so miserable, not even that can redeem her..

Just remembered another great 'companion' that i found entertaining. The sentinel weapon you get in NwN: HotU.

Older games Minsc (Baldur's Gate), newer titles Lydia (Skyrim). You're right about that and still, there's more to it. Guess you can just grow fond of her.

No fans of Democratus?

If i had to name one NPC companion i despise it would have to be Lydia.

All right, that was a brilliant story.

Kreia in KotOR 2. She takes the cake.

Honorable mentions:
HK-47 and Visas in KotOR 2.
Morte and Annah in Torment.
Edwin and Viconia in both Baldur's Gates (but they are given more character in 2).
ED-E and Raul in New Vegas.
Marcus in Fallout 2 (it's nice to have a clever mutant on our side)
Virgil in Arcanum (actually he's the only companion I remember from the game... there was a goodie-goodie dwarf and elven aristocrat chick... but that's all I can remember about them).

Minsc and Boo from BG2
Morte and Fall-From-Grace from Planescape.
Murray from Monkey Island, oh wait, he's not really a companion lol Pretty sure Murray existed before Morte though.

My diagnosis is you need to play more RPG's, stat!

Well - I love games where you roll up / create your own companions, however:

Older - Minsc and Boo form Baldur's Gate 1 and 2 - Butt kicking for Goodness!!

Newer - Leliana from DA:O - What a Voice

Sulik (and Grampybone) from Fallout 2

I just can't wrap my head around how camp Dragon Age is. It's like it is impossible to find a clip from it that's not situated squarely on that "don't know whether to laugh or cry" threshold.

Gavin was the first one that came to my mind, too. Though I recently started playing Morrowind with the Julan Kaushibael mod and I like him a lot.

If I had to chose vanilla companions, for some reason I like Kivan from BG. And just about every dog in every game. Dogmeat, dogs in Skyrim, dogs in Guild Wars, dogs in Torchlight...