Chill from Paladin's Quest, who forces her way into your party when you enter the town she's in, but will leave your party before you actually get into any combat. She has some unique equipment that you never get to use. Though, suspiciously, she has only 300 HP, at a time when other party members are on the verge of braking 1,000.

Dragon Quest 5 SPOILER ahead.

In Dragon Quest 5, the daughter. Thing is, later in the game you end up having two children, a son and a daughter. The son gets to be the legendary hero, but the daughter doesn't actually get anything, other than being a mage in a game where magic isn't that useful (barring the Echoing Hat, but that's not until the final dungeon in the original and never in the remakes). In fact, the game's handling of the daughter, and in fact of other female party members, feels rather sexist, not to mention that the main character has to be male, unlike DQ3 and DQ4 where you're given a choice.

There's also cases like Final Fantasy 6's Umaro and Gogo, but at least those two characters (especially Gogo) are mechanically interesting as party members, and Gogo is a nice reference to the previous game in the series.

I can't think of any characters offhand, but my first response is to theorize. Maybe they had a personality that was cut for budget reasons. Maybe they had controversial or unpopular content that was cut during testing. Maybe they were part of a quest/area that itself was cut, and now the NPC no longer is relevant. Maybe devs argued over what to do with them and in the end, couldn't agree, so the NPC got no attention. Maybe there were plans to make them relevant later with DLC that never materialized.

Just like deleting software from your computer can leave straggling files and folders here and there, so too could deleting game content leave NPCs and items still present but no longer useful. Might and Magic 8 was supposed to have a druid's quest, and had a druid's crown in it, but the druid class wasn't added, so the crown, still in the game, does nothing.

It would be nice if all games were super polished: all typos fixed, all links and quest markers verified, all NPCs doing what they're supposed to do.... but games are bugged, and polishing comes after bugfixing, and devs will/can only do so much. Sometimes useless bits... crumbs... remain.

T3-M4 in KOTOR is a droid without much in way of personality and communicates with beeps. It's only needed for story progression. That said, T3 can be useful as source of computer spikes or a skill monkey in a party.

There's also the Tracker skill in Might & Magic 3-5. It exists, and in MM3 and MM4 you can get it by finding a place where you can pay to learn all the secondary skills, but it doesn't actually do anything.

MM5 also has the Crusader skill, which you can get by starting as a Paladin (or taking a party from MM4 that has the skill), but it's not used and is only there for compatibility with MM4, where the skill does exist, can be learned via a quest, and is used at one point.

Also, in many games there's leftover data, like how Icewind Dale and Baldur's Gate 2 both have leftover data from the first Baldur's Gate.

I could also mention the Crown in Final Fantasy 1. It's an item that you're required to get early, and then when you enter a later (technically optional dungeon), there's a person who says you need the Crown to progress, and the game actually checks for it. Thing is, it's not possible, barring something like a hack or an arbitrary code execution glitch, to actually reach that point without first getting the Crown.

Or the Hidden Palace in Sonic the Hedgehog 2. It was planned early, and even had a music track made for it. However, it was cut from the final game, inaccessible without a cheating device, and not playable even if you do access it (graphics are garbled and the collision data is gone, so there's no solid ground). The music, on the other hand, remains and is accessible through the game's built-in sound test.

Mud in "Gothic".
I eventually killed him.

Well, interesting idea for sure, but the thing is, Final Fantasy IX got all of four disks. If anything, there was room for fat trimming. The other thing about Amerant: He's a PC. Not a NPC. I don't quite know how one would fix his lack of an interesting contribution without a radical redesign.

Heya! It's me, Imoen!

A PC/recruitable from Baulder's Gate?

Does anybody know the story of the mech suit in Jak 2?

Indeed. And she has absolutely no dialogue beyond the conversation where you recruit her. We do actually know why she's there, though- it's because the developers realised really late in the process that good players who didn't want to recruit evil NPCs wouldn't be able to get a thief for their party until quite a way into the game, so they added Imoen at the last minute.

Nobody else in the party ever acknowledges her existence, she says nothing, and yet she became so popular with players that she was given a major role in the sequel's story.

Xenogears

Rico

Yogurt in Shining Force is easily the most useless character I have personally encountered in a game.

First there's the fact that getting him to join your party requires completing a series of encounters in different locations that can be missed because you can't go back to prior town.

Your reward is a hamster with 1 hit point that cannot progress past level 1. If he does manage to kill an enemy in battle, you get a Yogurt Ring that can be equipped to another character to make them look like Yogurt. You could technically repeat this process to make all of your units look like Yogurt, but there's no benefit to having a Yogurt army.

One thing is that this character was *intended* to be a useless joke character.

On the other hand, you have a case like the Fighter from Ultima 4 (Geoffrey if a companion), who:
* Can't use any magic (fair enough)
* Can't use any magic weapons
* In particular, this means can't use any ranged weapons that work in the Abyss
* In a game where ranged combat dominates because you can either move one square *or* attack during your turn

Essentially, he's worse than everyone else except the Shepherd, who is clearly intended to be a weak character.

I usually kill her so I don't have to deal with her popping up but she seemed useless to me. Hell, I wouldn't even use her in Baldur's Gate II, if I didn't have to.