All this is news to me, perhaps my Shepard being woman changes Tali thing.. Saren, not so much. Some of those games are full of things and you thought that you saw it all.
Usually.. I try to talk my way out, in my opinion more interesting that way than kill everyone that come in sight. Well.. I always had to hit that scientist in ME1, pretty beginning.
"we are doomed!" "oh, shut up." *smack in the skull*

In the first freespace I cried when the Galatea was destroyed.

fear can be an emotion...
When i was a kid playing Monkey island 1 on my amiga... I remember being dead scared of the talking severed head on guybrush hands... i remember closing my eyes when it smiled...

Also the last few sceans of Wing commander 3 when you one by one lose all your wing men and your breifing room is all empty. very sad moment...

after so many years... geting to install monkey island again on my pc... the starting theme tune brought a tear to my eye...

After finding your father in fallout 3... you have to watch him die and be powerless to do anything. It is so not fair.

On the Amiga there was a WWI plane simulator called wings.... I started a charicter and called him The Yellow Baron mimicing the natzi red baron... I got my chariter promoted to top ACE in the squadron and promoted to leftenent cournel with all medals.... i was only one promotion away from top rank... and i got shot down,,, i had no save... i lost the game and i was never able to replicate that success... The scean of the dead yellow baron and blood dripping down the side of the plane as it hurtled into the ground was an image that to this day i cannot forget... it was a bitter loss

There are only 3 instances where I cried when playing a videogame

1: Warcraft III: Grom Hellscream's death cinematic

I dont think any more comments are needed here

2: When I finally completed Gradius V and the credits Rolled

That was...truly something...

3: Klonoa: Door to Phantomile ending cinematic

This one deserves a special mention because it's essentially a "Kid's game" and yet however this game gave me more emotional attachment and feelings than any other game I have played. I'm not going to spoil anything - Just play it and experience it for yourself

that was my favourite scene in the game, brilliantly done

Many, many, many.

All of Planescape: Torment. All of it.
Significant portions of Mask of the Betrayer.
The ending of FFX.
Most of FFT: War of the Lions. The translation is almost beyond words; it is matched only by that in XII. The moment in the game that really stuck with me, when I really realised what a masterpiece the story is, was when Ovelia was told she was an impostor. Was it a lie? Who knows. But the mere idea that it might be true... chilling.
Many parts of FFVII. Been a while since I played it.
The orphanage scene in FFVIII. I really should replay that game.
The end-of-disc event in FFVI. Yes, I know there was no actual disc swapping involved, but I can think of no better way to describe the massive event that occurs on the flying continent.
Braid's story initially failed to really move me, but once I attained the secret ending... The alternate interpretation offered was very much to my liking.
Zeno Clash's grand reveal. Didn't think you'd get a resolution, did you?
The assassination targets in the first Assassin's Creed. Each one offered a lengthy philosophical monologue after their death, something that felt strangely fitting.
The choice on Virmire in the first Mass Effect. One of the best things I've seen in a video game.
Several scenes in Mass Effect 2 - actually, make that most of them. Game of the decade, if it had been released a month earlier.

The list goes on. I tend to gravitate toward games with good stories.

The shocking destruction of the world you start out from in Homeworld was very moving.

Starcraft 1 and the Starcraft 2 Cinematic that depicts the event of leaving Kerragin to face the swarm... alone.

The destruction of Aiur in the Brood War Campaign.

The corruption of Arthus, and subsequent Murder of his father, as well as the death scene of Grom in Warcraft 3.

The exile of the Vault Dweller at the end of the game in Fallout 1.

I'm sure theres more but I can't think of them right now.

Breath of death VII (that indie game)
All those mutated lives had to go because some bearded pixel wanted the past back.
Reminds me of doctor light.
He wasn't light, he was a bit on the heavy side.

I miss the days when guys weren't so proud of how they get emotional over everything.
Crying when your kid dies of cancer is one thing. If you cried when Sephiroth killed Aeris, you need to go out and buy a douche to wash your pussy.
just saying...

When I found the Chainsaw in Doom.

I cried with giddy joy :3

This...it was a true WTF moment..i remember staring in awe as Sam was walking down the street during the credits, saying to myself, Really?......Really?....REALLY?

While we're on the topic and you brought up WC II, I would say each subsequent Wing Commander definitely had an emotional heartstring-tugging moment:

Wing Commander III: Hobbes betrayal. When I first played WC III I was floored that this had happened. I cut my teeth in the WC universe with WC II so as far as I was concerned Hobbes' reputation and fealty was beyond reproach. I stood up for him during each branching dialog option. I couldn't climb into a fighter fast enough to hunt his turncoat ass down when I saw Cobra bleeding to death there on the flight deck. Then of course, twisting the knife in, Vaquero dies as a result. Revenge has its drawbacks...

Wing Commander IV: Vagabond's death. Vagabond was my favorite character in the series, so his scripted death was a huge blow.

Wing Commander Prophecy: Death of Hawk. The quality of the WC had taken a severe nose-dive after the high-water marks of WC III/IV, though Prophecy still had its moments, mostly on account of return appearances by veteran cast members of the series. Hawk, played by seasoned character actor Chris Mulkey, was one, so I was pretty bummed when he was unceremoniously killed off. Of course, all the "new" fighter-jock pilots lived, people I uniformly didn't care about and had all the personality of wilted lettuce. Ingrates.

What a great series, though. The FMV era's finest hour (along with Privateer 2). Nothing has filled the space-sim vacuum since, or even had a good game to the genre's name, Freelancer excepted. However, that was eight years ago; such a pity.

You get your chance at revenge anyway.. If you choose not to chase him down you meet him on one of the final missions and he orders his wingmen away for a 1 on 1 duel. From what i recall anyway.

And if you want a good game like Wing Commander Starlancer was pretty awesome.

http://www.youtube.com/watch?v=zfJxAo_LC9M (intro)
http://www.youtube.com/watch?v=bSKVJM6IXxQ (1st mission)
Chris Roberts was involved along with Digital Anvil who did the WC film CGI

Oh I've thought of another one that made me laugh my arse off every time, in Mass Effect 1 & 2 where you can punch out that reporter kalisah al-jalani. Ever so satisfying and the opportunity in ME2 to see its not just YOU that does it... awesome stuff. They've got to have the option in #3 (ideally accompanied by an achievement)

Especially with the use of the music, initially seemed very out of place for the kind of game but worked extremely well and tied into the teaser/advert they did a few months ago.

Sgt. Johnson's death at the end of Halo 3, Capt. Bannon death in World in Conflict and what happens in Gears of war 3.