Goldeneye was definitely the first FPS to established the genre on console, it made it popular, Perfect Dark perfected it and Halo drove it to the online community.

Half Life 1 was turning point in genre.

Bioshock, easily.

Counter-Strike.

I forgot to mention Fallout 3 when earlier on this board I only mentioned Metroid Prime.

These 2 games don't just fit into the FPS genre, they could fall under a range of genres. so I don't know if they count to a lot of people but they count for me because mono-genres tend to be uncreative in their nature, therefor I would promote these 2 titles for 'best' FPS and not best 'most standard' FPS. Also FPS games tend to a mixture of genres anyway as they could all fall under action too. Fallout 3 and Metroid Prime are just unique hybrids which makes them stand out and therefor making people question their genre.

Yeah the Prime games are tricky to categorize as they straddle several genres.

I personally don't really think of them as FPS games, but if I did I'd add all 3 to my honourable mentions shortlist, they are amazing.

Neither Metroid Prime nor Fallout 3 are FPS.
Fallout 3 is an RPG. You can play it without guns and even try playing totally peaceful (pretty tough though). Or you can use VATS which makes it more or less turn based like.
Metroid Prime is a 3D Action Adventure, more precisely a 3D Metroidvania.

Forgot about this one!

I think it gets overlooked because while it was awesome at the time of release, it was very quickly overtaken the arrival of the 6th gen systems and Halo.

It's kind of like the last battleships to be made; they were great for what they were, but were quickly left behind as the aircraft carrier took over as the primary capital ship of the world's navies.

Sadly this is my experience as well. I played it on The Orange Box for the first time. After a while I began to wonder what the big deal was. Then I just went back to playing Portal.