Regarding Rokugan. 3rd edition L5R allows you to play Bushi (warrior), Shugenja (priest), Monk, Courtier, Shinobi (spy/assassin), Yojimbo (body-guard), Ronin (duellist, warrior, or Yojimbo).
That said; I would love to have this setting with a simpler system, since I personally hate dice pools.
As for conversion of Eberron. The main problem, as with any D&D setting, is magic. You would have to create or convert D&Ds basic magic, the spells that are Eberron specific, and the Articifier class spells. It would also be a good idea to convert some of the different classes abilities into some sort of Heroic abilities or spells, which you can easily tie to some sort of archetypical template, if you want to preserve some of the classes abilities at all (for example a Paladin template gives you Lay on hands, or you buy it with Hero Point).
It is pretty stragith forward to convert the abilities of the races, since they use much the same scale, you can just use the ability modifers. STR = STR, CON = CON, DEX = DEX, INT = INT, POW = WIS, CHA = CHA.
Roll 3d6,2d6+6, or what you prefer, and add the modifier from the race.
Some racial abilities are also going to be a problem, such as the different metal bodies of the Warforged, which grants damage reduction, such as 2/Adamantium etc. However, that specific aspect of the warforged is probably most easily directly converted into permanent armour. Since the weapons deal pretty much the same amount of damage in Eberron and RQ, you could just convert DR directly to permanent AP.
In many ways, I think RQ would be a better system for Eberron, than D&D. Because the setting seem to have originally an innate flexibility, which is partly destroyed when you force the different D&D classes etc. onto it.
As for doing Dune with RQ, what is needed is basically rules for the technology, description of technological devices, rules for vehicles, the "magic" of the different supernatural phenomenon that the characters can come to master.