All published UA fares earn miles. I believe this includes F, A, C, D, Y, B, M, H, Q, V, W, S, K, L, and T (but not if bought from a consolidator)
C, Y, B, M, H are upgradeable on international flights.
All others are in fact upgradeable domestically unless bought via consolidator, e-fare, priceline, or the equivalent.