I once began the task of converting the Dark Sun campaign setting for use with the Pathfinder Ruleset. I didn't finish the task in the end, as the players decided that they would rather play Forgotten Realms instead (which was conveniently much more easy to adapt).
Anyhow, along the way I found a couple of other conversions of the Dark Sun rules - one for D&D 3.0 and one for D&D 3.5. Now, of course, these won't be of direct use to you in terms of the rules - but I found that they provide a great template for the bits of Dark Sun that you will need to convert (as opposed to the story-based bits that you can simply leave in their current form).
You can find the conversion for D&D 3.0 in the form of Dark Sun 3 on athas.org. The table of contents (and the PDF) shows the sort of things you will need to account for in the new system. For instance, Races, Classes, Skills, Feats, Equipment, Adventuring, Magic, Psionics, Spells, Powers.
You will have to hunt for the Dark Sun 3.5 conversion, as I believe it appeared across a number of issues of Dragon magazine. It comprises a similar set of content however, so I suspect the above document shows the majority of the elements you will need to consider when doing your conversion process.