In the Najdorf:

In the Old Classical Sicilian:

The only difference between blacks set up is that Qc7 in one and Nc6 in the other. In response, white plays Qf3 against Qc7 and Qd2 against Nc6.

Why? What are the reasons behind the different placement of the queen?

White plays Qf3 to discourage ...b5, due to the threat of e5...

Pretty much on the right track there Crazychessplaya.

The move Qf3 is mainly designed to discourage black from playing an eventual b7-b5 because of tactics on the diagonal and will make central strikes like e7-e5 and f7-f5 more threatening when black plays b7-b5.

It's important to notice when black has put hes knight on c6 hes usually going to play in a more slower manner and the attack on the queenside will not be as dangerous with the c-file already closed (black usually wants to develop Qc7, b5, Nbd7 if he wants to attack on the queenside) and often blacks plays very solidly by developing like Nc6, Bd7, Qc7, 0-0-0!?.

When black creates this setup it's effective to have the heavy pieces placed on the d-file pressurizing the weak d6-pawn and a common concept for white is after black plays the move Bc8-d7 (plotting to play Nxd4, Bc6 to free hes position a little) white avoids exchanges with Nd4-f3! and threats to undermine the d6 pawn with Bg5xf6 which is often quite unpleasant for black to deal with.

Thats another thing I dont understand - if black wants to play Bd7 Nxd4 and Bc6, why show your cards with Bd7 first, surely play Nxd4 and then Bd7 Bc6 ? Is the issue that white plays Bxf6 and now gxf is forced due to the d pawn?

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 Frequently in the Richter rauzer (classical sicilian with Bg5) you do chop the knight on d4 to remove some of the tension.  I personally do not favour the line in the diagram as a6 doesnt fit - Qa5 is better than Qc7 usually.  Also you can sometimes recapture with the bishop on f6 and let the d6 pawn drop as a sac for activity.  Not always, mind.

So a6 in the Richter Rauzer is no longer fashionable? I got these positions from the chess.com database, not sure how up to date they are.

The line I play would have Black castled instead of a6 and he would chop the knight here then play Qa5

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That can actually be the correct way for black to approach the position sometimes, it really just depends on how the position looks like. Sometimes it doesn't work because of Bxf6 ideas like you mentioned which can be a problem but also because of thematic ideas like f4-f5 and e4-e5 which can turn out to be more effective with white's queen centralized on d4.

d4-d5?  Do what now?

Also I just remembered that also an issue in the classical sicilian is that the knight on d4 is constantly attacked so it would be quite tricky to create the f4, Qf3 setup even if you wanted to, but it seems to make more sense to develop the queen on d2 anyway.

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ah, well spotted, updated!

Talked to much about the benoni recently I guess. xD

You may prefer to play Qd2 against the Najdorf too, but after 5...a6 6.Bg5 e6 7.f4 Be7 8.Qd2, there is 8...h6 when 9.Bxf6 gives the bishop pair without damaging the pawn structure (compare with the Rauzer), while 9.Bh4 runs into ...Nxe4!

I've switched to the line Karpov used to play 

Now that's looks a lot more like the kind of variation I would prefer!

Though I probably would delay f2-f4 and perhaps just try to play positionally with Be3, a2-a4-a5, Qd2, Rfd1, Nc1-a2-b4-d5! *dreaming*

Of course it's just a matter of taste how to approach the position. ^^

Which moves Conzipe? 8. Be3 and 9. 0-0  with 10 a4 ? 

Haha, I'm not sure, just throwing out ideas on the top of my head, not sure if the plan is even good as black might even have some clever way to prepare d7-d5 for example. I basically know nothing about what the theory says here but it looks like you could squeeze a bit in this type of position.

However if this kind of positional plan doesn't work and f2-f4 turns out to be forced I would probably look for something else. Luckily I don't play 1. e4 (and even when I do I usually play some anti-sicilian) so I don't have to worry about the najdorf. However if I someday change to playing 1. e4 then I would perhaps start with looking at some kind of line like this. ^^

I think its the best way to play against the Najdorf. Target the weaknesses black has created with his stupid pawn moves ;)

What Conzipe was describing Karpov was playing in the 80's when he was still a 1.e4 player. Not considered very critical these days, but has worked well enough for me at my club player level.

I've switched to 6. Bg5 now, and am having more success. 

Indeed, after having to discuss this line a bit further it seems black is always able to create sufficient counter-play against this kind of squeezing plan. Najdorf is a strong opening!