I agree with many choices made here, so here are a few others to jog your memories. And this took much longer than I thought.

Best/Worst plot twist
Best
Final Fantasy 3 (or 6 depending on your country). The team loses and the world gets destroyed...didn't see that coming did you!

Worst
Divine Divinity. The 'plot twist' that the Boy Prince was possessed...like I never saw that coming. In fact could it be counted? In that case I go for FF8 with the everyone was living together at the orphanage thing. HA I spoiled it all for you!

Best/Worst fight
Best
Modified Throne of Bhall, against the Firegiants army.
Worst
The Chaos Lord guy in Divine Divinity. He went down way too easily.

Best/Worst city
Best
The Old Camp in Gothic. Technically not a city, but it was fantastic. Everyone had a schedule, everyone knew each other so annoy one and his mates would get involved.
Worst
Britain in Ultma 9. Don't get me wong, I kind of liked it, but it was tiny and no one didanything. It was supposed to be the capital but only 15 people lived there!

Best/Worst npc
Best
Marcus because he could kill anything with a Bozar
Worst
Marcus because he could kill anything with a Bozar including my party

Best/Worst weapon
Best
It's a mod for Morrowind. It features the Talking Sword Lilacor from Baldurs Gate2. Whoever recorded the voice for it deserves a medal. Imagine a nasally voice "You want to know you how I got here..hmm? Well I'll tell you anyway"
Worst
Excalipur heh heh if you know what I'm talking about well done.

Best/Worst spell
Best
Call Lightning from PST. The screen went dark, a massive bolt cam down, the whole screen shook. Such a common spell but it worked great. In fact many spells in PST looked great.
Worst
Call Eden from FF8. The most powerfull summon spell and it took like 20 mintues to run the animation. it was just silly and made the spell useless.

Best/Worst skill
Best
Finesse in Fallout. I just liked the bonus to citicals so much
Worst
Any thief skill other than traps/locks. Who has time to sneak or backstab in a party based RPG

Most hated npc
The somewhat disturbing 'gay' convict in the old camp in Gothic who followed you around and kept bugging you to do 'stuff'.

Best/Worst quest or sidequest
Best
The arguing farm hands in Gothic 2. It wasn't really a quest, and it couldn't be completed as such. But it was so funny to wander back forward repating each persons comments until they got so angry and started fighting.
Worst
The Kidnapped parents in divine Divinity. The game removed control from the Player at a key point...what's the point of the quest then.

Hardest quest
Any of the 8bit and early 16bit games, before Automaps were invented. They all had a damned maze in them to increase longevity of the game. Bah!

Hardest game to beat (boringness doesn't count)
Every play Bards Tale 3. IT was uncannily hard, at least the beginning was. A nine level dungeon that many thought was the whole game but was a fraction. I vaguely remember fighting the first boss and it took forever because the only way to beat him was using 'cheat' tactics by hiding in shadows repeatedly until you did the equivalent of rolling six sixes, allowing a slight amount of damage to the enemy.