I feel like Rebel Assault II was really popular - I never played computer games, but I did get through pretty much the whole thing at a friend's house. The combination of well-known cheats, a reasonable storyline for 10 year olds, and gameplay that didn't stress the computers available to most kids probably made it fairly common, while things that were a bit less accessible both story-wise and tech, like X-Wing vs. Tie Fighter, didn't gain as much traction (even though that was the only one of the X-Wing series I ever actually played).
As popular as Rebel Assault was, I am going to say that the X-wing and Dark Forces series were much more popular.