No order specifically but

1. Halo 1-3: Other games in the series are still pretty good but I don't think you can beat the original three.
2. Half Life 1/2: Excellent set of games too bad there wasn't a third . Despite being the same series I find both play quite differently
3. Doom 1/2: Honestly I liked Doom 1 more but still really good games
4. Quake: Really liked the first, 2nd not so much
5. Team Fortress 2: too many hours invested, I had to mention it.

Went to buy this just then, turns out its already in my Steam library.

I had never even heard of it, must have gotten it as part of a bundle

Word of advice - decide early how you want to handle franchises/sequels and flag that for readers. 

Also be clear about your criteria:

1. Games that were great when they launched versus games that are great now
2. Whether mods will be counted, and if so do they replace a poorer original on the list
3. If you make ANY attempt to give a little love to all systems just because - admit it up front
4. Games that are incredible and have heavy shooting elements, but are better considered in other genres (eg. Mass Effect)
5. The treatment of sequels/franchises

Options for point number 4:

• Only the best game from a franchise will be eligible.
• Every game exists in its own right and therefore multiple games can appear on the list

100% halo....... by a land slide

I recognise its all entirely subjective, but Resistance and Killzone are sort of what I was referring to when I talked about attempting to give a little love to all systems just because.

Resistance had a few really good games...Killzone 2 was also recognised as being pretty great.

But top 50, of all time? Its just hard to see. You so rarely see these games mentioned in the same breath as the real cream of the shooter crop. Don't get me wrong, Playstation has an illustrious history of games and franchises that are exclusive and appear on top 50 lists (hell, top 10 lists). Just not so much the shooter list specifically.

Of course it's subjective.  How can it be otherwise?  I mean, you've got Perfect Dark listed, which I've never played before, so I looked it up on Youtube--and, quite honestly, it does not look like a good game.  Influential, perhaps, but I can't imagine it being recommended to anyone.  Just that few minutes of video gave me a headache and made me feel kind of sick.  I'd certainly take Killzone 2 or even 3 over it in a heartbeat.  Those games brought a unique and gritty vibe and had some of the best feeling weapons I've ever encountered in any FPS.

That's only because not that many people have played them. I think they are better than stuff like CounterStrike or TF2. People would, in general, choose the latter because that's what they played. You just had to play the MP to realise that they're very unique games. I still remember the 60-player skirmishes in Resistance 3 or the variety of weapons and powers of Resistance 3 and KZ:SF. Great stuff.

Perfect Dark gets my highest recommendation.

#1 Quake

then the rest, nothing comes really close.

It woudln't be that site if not such a post was made