I can compare them because I like'm both and they're part of the same universe :P
Also, I have to tell that April Ryan and Crow disappointed me a LOT too :( But once the game is settled you go with it.
But Dreamfall is different than TLJ, and I like its new approach, especially this new "let's play with 3 different characters"... It was more mature too, but kinda different. I read the same things I've thought in the Ragnar Tornquist interview on rockpapershotgun.

Final Fantasy games seem to give me the most emotional impact. When Aeris died in FF7, I had a hard time moving on with the game for a while; FF3 and 8 were also brilliant.
System Shock 2 scared the crap out of me.
The end movie from Descent 2.."To be continued..." NOOOOOO!!!! That was a long wait.
The Half-Life series was also very well done.
The Fallout series, of course.
There are so many others I'm forgetting, but I tend to put more stock in the emotional impact of games than I do movies because I'm a part of it. Movies are passive; I've watched a lot of scary movies and very few of them have truly scared me. But when I was walking through the corridors of the Von Braun at 1:00 in the morning with all of the lights off, it had an impact.

I'd say one game that affected me was sanitarium.
I really don't want to spoil it for anyone who hasnt played it before but its one of the most intriging and disturbing games i've ever played and i'd whole heartedly reccomend it. Its about a mans fight for sanity through the real world and his mind. It really makes you think.....
just one example from it.... (spoiler)
at one point your sub conscience puts max (you) back in his childhood memories, which are twisted and skewed like a vivid nightmare, filled with ghostly apparitions of his family. he ends up talking to his sister, whos ill in bed and asks him to get her favorite toy from the attic. after a lengthy search you come down the stairs, toy in hand ready to give to your sister, only to find you were too late and she'd passed away. My description doesnt really do it justice, you really feel for them, its a genuinly touching moment.

Oh yeah Sanitarium was excellent. I remember the end, I was like... wait what it was that? Holy crap...
And the memories and psychedelic nightmares mixed with reality are just astonishing.
It reminds me another adventure game, Phantasmagoria 2 (the first was a bit crappy imho). This one was fantastic until the end, the big wtf scenario part with aliens and stuff. Otherwise I shit my pants all over the first episodes.

I'll agree on mostof your points - but Dreamfall more mature?! No sorry - where were the Lesbian Landlords? The natural swearing? The very adult emotions and stories of friendship, support and sacrifice? Where was anything like the Spirit Dig with the Banda people, where she converses with her younger self? TLJ was by far the more mature game, in fact one of the more adult games ever released - in the good sense of 'adult'!!! Dreamfall was totally tamed down for the console market!
There is a chasm developing between gamers who have only played for 5 years or so and those that have played for 10 or more. So when compared alone Dreamfall is a mature game, and when compared with games of the last 5 years it still is, but go back to pre 2000, and it is not that special at all. And certainly Dreamfall would have scored in the 30's if it had been released in the 90's reviewers back then, more independent than now, would have been mad at the lack of gameplay, which back them was king! Not like now when graphics are king and gameplay a poor second!

At the time, that was one of the best choreographed scripted events in gaming. In fact, it may still be.
Strangely enough, the next time I played FFVII I encountered an opposing emotion. I knew it was coming. Instead of shock and loss at losing a sympathetic character, I started to feel guilt for playing. There was nothing I could do to prevent the events of the story, and therefore every step I took towards that point in the game was a step closer to her death. In a way, my very actions were killing her. The only way to prevent her death would be to stop playing.
I didn't.
There's a certain meta-level to the interactivity of games which makes the player more responsible for the events that take place, and it's intriguing to study its effects.
Teph

The Beast Within: A Gabriel Knight Mystery
It's not so much the scenes that really impacted me, but rather the musical score. Even though the piano theme gets played repeatedly, I never, NEVER got tired of hearing it. Couple the music with the backdrop of the furnace scene, and immediately my eyes turn on the waterworks.

Oh yeah... I felt in love with Mona <3 The first ending is sad... I was so sad that I did it again in hardest mode, good ending! whaa o/
Film noirs video games are just awesome.

By choosing Bladerunner I give you +1 point - even though you don't need it! :)

Half Life 2 Ep 2:
Fighting my way through the undergound garage with Alyx. It's pitch black, flashlight only illuminates so much for so long. Killed last zombie, reloading clip, flashlight dies and I hear ANOTHER ZOMBIE!! LOAD DAMMIT FLASHLIGHT ON LOOK AROUND CAUSE IT'S CLOSE.................
It's Alyx making the noise, she says something to the effect of 'Got you that time!'
It scared me, pissed me off then made me laugh out loud all in a span of seconds.
Loved that one.

The end of disc 3 in Final Fantasy VIII. The vocal version of Eyes on Me, with everything that had happened in the game with the Laguna - Julia backstory, left my throat dry and almost tears in my eyes.
<MORE SPOILERY THAN A LOT OF THIS THREAD>
I was also really devastated at the end of the Companion Cube level in Portal. At least he was alive and well at the end cutscene. Cubey didn't die after all :)

Baldur's Gate 2: I felt damn disappointed when Yoshimo turned out to be a traitor. All my time in developing a master thief, wasted!

In Deus Ex 1: Being forced to choose between executing Juan Ivanovich Lebedev in cold blood or killing Anna Navarre in cold blood. Realizing that all those guys you head-shotted as rebels earlier in the game were actually the good guys. Having to dust your now ex-co workers in UNATCO. Realizing that your ex UNATCO pals no longer see you as a person but merely an enemy. Also - no matter what some scum bags still remain no matter what you do (exactly like life) - example the illuminati members still in existance in dx iw.
For sheer retarded joy: using the gauss gun against buildings, vehicles, enemy agents, bystanders in Syndicate. The amusement of using the persuadertron on half the populace of any given city.
FEAR: Alma and the Point Man's relationship to her. The sheer tragedy of her life and death and her (quite understandable) fury at her treatment. Plus probably the most atmospheric game I've ever played.