Half-life 2 and episodes then Bioshock 1 then Resistance 3
If you don't mind dated visuals, Half-life 1 is still great and so is Nolf, can't go wrong with Stalker either.

Killzone.

The Metroid Prime trilogy.

Half-Life followed by Metroid Prime

Porps for mentioning No One Lives Forever :D

the half life love is the falacy of past memories, its like when people say morrowind was better then skyrim then it turns out to be a load of crap. if you play half life 2 right now you will probably be like wtf... it has a few good things but its nothing special ( actually pick up the orange box for $10 or so and try it on 360/ps3)

unless this is half life 1.. havent played it tbh

anyways i picked halo. halo 1 is still the best console shooter.
Kinda feel like bioshock shouldn't be on the list because it was a single player game, so it should have the better story. but even still i didn't like it to begin with ( nice setting though)

Half-Life, then Metroid Prime.

Funny, I replay Half-Life 1 & 2 on at least an annual basis whereas I thought the original Halo was a pile of hot garbage :/

Unless you actually play through those games in current times and still find them better than the current alternatives. Your argument would be valid if people based those feelings on nostalgia alone after years since they last played them, but in most cases that's not what happens. 

Personally, I still play both Half-Life and Half-Life 2 (I still got the full Orange Box installed on my laptop, heck that's the first thing I install everytime I switch laptops) and I play a lot of Abandonware and retro games that I still find much better than the current alternatives. 

Newer experiences don't automatically mean that they are better than the previous ones just because they're fresher. Heck, even some newer games are less substantial in both content and complexity than older games. For example, you give the Skyrim vs Morrowind comparison; while Skyrim is indeed an amazing Elder Scrolls game (my personal favourite, it dethroned Daggerfall), it doesn't have a lot of the complexity that Morrowind or Daggerfall had and in some aspects it has even less content, though it's much better executed and streamlined than those two games (except for the UI part), so while some people will adapt better to Skyrim, others will still prefer Morrowind or Daggerfall to it.

I'll end by saying that it's not a good thing to encompass the opinions of everyone who sees an older game as being the better alternative to a genre or anything else just by claiming that it's due to Nostalgia alone. That can be insulting and demeaning to the capacity of critical thought of a gamer.

I played HL2 for the first time just over 2 months ago and it is mostly because of HL2 (and the Episodes) that I mentioned it in my choice along with the Metroid Prime series. It was only a week prior to that that I played Half-Life for the first time too, but it is quite dated now so I don't rate it that highly on it's own, however for a 13/14 year old game it is still very good.

Also, I have nothing against dual analogue (or less on the N64) FPS in general, but after playing HL and HL2 with the mouse I really can't see how I would enjoy playing it using an X360 or PS3 controller, it just seems wrong.