In QL cypher has more major lan wins and is the last lan champion. In both criterias rapha got second place. However, it'd be unfair to say cypher was the clear best because they are very close in achievements and in overall level, to the point it might change depending on the amount of major lans hosted and if rapha wins them all, so I'd say it's a moral tie but objectively cypher is the best.
That means if id software were to give a special prize to the best QL dueler (for example when the game is shut down) it would have to go to cypher anyway, or share the prize if you want to go emo.
Anyway, my point in that post is that people blindly believe that rapha is the clear best and this and that. In reality he is not the clear best and furthermore he is second, though not second by that much.

In Q4, tox got the most major lan wins and no one was really close. He was the clear best.
The only thing that could be added is the 'what ifs', in the sense that cooller was the one that had the edge over him at the beginning of Q4 and that avek showed lots of potential. Makes one wonder how things would have turned out to be if cooller didn't have visa issues and if avek was born 5 years before.

In Q3 you could say there's eras. In the first one there were several champions, including zero4 and cooller, and in the second one cypher dominated. That means it's uncertain who got the historical achievement (would have to search quite a bit. Mind you it would only players with more than 3 major lan wins so lots of names are discarded immediately) and it's 100% certain who achieved the highest skill, which is cypher by far.

In PK voo won the most tournaments of the sole big competition I can recall, officially earning the title of pk cpl tour champion, not fat. Google it up if you want, the trophy was given to voo. As he won major lans voo was the historical champion. As for who got the highest skill it would have to be contested between voo and fat, because it was just like QL is right now and fat won the last stop which was the biggest event.
My point here is that this is similar to what is going on in QL, in which noobs think rapha is the clear best. People think fat was the clear best and dominated and etc., but fact is it was contended and that voo won the tour. The only difference is that in QL rapha's exaggerated reputation is because of community and player hype, whereas at least in fat's case fat earned that reputation by winning the last stop, that was aired on mtv and had the biggest prize pool of all the lans hosted.

In Q2 the clear best in everything was Purri, back when it mattered and before QL started (QL pretty much killed all previous quakes). Quite easy to tell really.
You could say thresh was this and was that, but at the time the US and EU simply didn't clash. I remember one showmatch and that's it, which was online between purri and some top1000 player. Also thresh lasted in q2 for less than 2 years, in a game that lasted at least 10 actively and that bloomed (or rather started) after thresh's period.

About QW I don't know much. However it has to be said that the game rules changed entirely when QW was released, after Q1. Comparing 1996 quake1 to 1996 (same year) to 1998 QW cannot be done, and besides the sole known lan (the ferrari one with only us players) Q1 did not have notorious competitive activity. The game really started with QW, not before.