I think Eberron would work well with many different systems, depending on what setting themes you wanted to focus on. Personally, I think 4E D&D does a good job of handling Eberron.
Things that I think are essential to Eberron:
Magic replaces technology, and is fairly common.
Dragonmarks and the Dragonmarked Houses
The Draconic Prophecy
The Last War and its effects (including The Mournland)
The Five Nations and their ongoing intrigues and rivalries
Eberron Religion (characterized by having two powerful public churches with potential for corruption in both, as well as a small number of other religions)
Things that I think are essential to Eberron:
Magic replaces technology, and is fairly common.
Dragonmarks and the Dragonmarked Houses
The Draconic Prophecy
The Last War and its effects (including The Mournland)
The Five Nations and their ongoing intrigues and rivalries
Eberron Religion (characterized by having two powerful public churches with potential for corruption in both, as well as a small number of other religions)