I never played in a war so never used any such system, but here is what I know.
Official rules at this point are limited to the Miniatures Handbook, which I hear is not that great and fails completely beyond skirmish level. An upcoming book from WotC will cover the topic, but that will take some time to publish.
There are a number of unofficial 3rd party suppluments covering the topic. These include Fields of Blood, Empires & Strongholds, Cry Havoc, the Slavelords of Cydonia + Grim Tales system, Merceneries, and probably more. The one to choose depends on your preferences.
If you want a greatly detailed system for relatively small armies Cry Havoc I think is good. It also includes a more abstract system, for faster war resolution. I personally don't like it's "d20 combat enlarged" approach.
If you want an abstract system for quick combat resolution that still allows some strategy, I am imressed with the Slavelords of Cydonia approach (using EL to determine strength).
I have heared raving reviews on Fields of Blood, so you might want to look there too. I caution you that the book also entails a kingdom-management system (as does Empires and Strongholds), which maybe hard to entangle from the war rules (or not, I don't know).
Of course, Diaglo undoubtebly will swear by the 1e system
I'm sure people more experienced in the matter than little old me will come by shortly and correct my mistakes. At any rate, there are several products available but none are official, and I'm not familiar with house rules on the subject.