I'm running the aforementioned E6 Dark Sun campaign, and figured I'd chime in with a few of my own observations from the GM side of the screen:
1) First, realize that Dark Sun was created with 2e rules in mind, and quite often conflicts with some pathfinderisms. Be prepared to change rules to fit the themes you wish to present to the group! I think it's best to tell the group in advance that this may happen, and to discuss any changes before you implement them. In my campaign, I decided I hated 0 level spells being infinite, as they went against our theme of scarcity. I allowed a minor rules change that limited the number per day; in exchange (so I don't nerf player decisions) I changed the rules a bit and let the players pick which benefit they could get.
2) Throw away some time-honoured traditions. Axe alignment and alignment-based effects; they're useless for Dark Sun, and actually get in the way (there should be no lawful good dark sun PCs!). Play around with the races a bit. And most importantly, lose wealth by level guidelines. Normal D&D is based around the idea of PCs getting progressively better; in Dark Sun, that should not be the case. PC resources should ebb - big scores contrasted with big losses. In my current Dark Sun campaign, the party just found a huge score in resources - a metal longsword (masterwork, to boot!), several magic items, potions galore, and something like fifty silverpieces in change (the equivalent of around 500 gp in other campaigns, but actually even more), as well as some gems of indeterminate value. However, they have also in the past faced weapon breakage, losing goods to raiders, and other wealth losses.
3) Don't just focus on rules. When GMs start trying to "convert" Dark Sun, they fall into this rule trap - how do you model half-giants, how do you model defiling, how do you model thri-kreen? I think part of the appeal to modern GMs with Dark Sun is the fact that it requires a lot of rules tinkering, and admittedly, that is part of the fun. But you really need to pay attention to the world itself, and what you want going on.
The way I have my campaign set up is as a sandbox. It is based on encounter tables, and each city has six events that could occur when visisted - I roll the event before the PCs get there, and roll with it. There are also a few ongoing major plots that are occuring whether or not the PCs are involved (such as the always present Tyrian revolution).
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Anyways, I have been running this campaign since september, and I can honestly say it's been one of the most enjoyable and rewarding campaigns I've ever run. In the previous post, Blargney links to our wiki. We have a PDF that's around 100 pages long that could be worth looking at, though a big chunk is focused on the E6 rules, and we leave out some of our house rules that I haven't gotten around to transcribing (such as our peculiar way of stat generation or our multiple PC rules). Bear in mind that some of it has been taken from other sources, and not all has been written by myself.
In any case, it's a good place to start to see how someone else has done it.
