I have run a few games for just 2 players to good effect. I think almost any game can be run for 2 players, but some lend themselves to the effort more easily.
Savage Worlds is at the top of the list. It is easy to run, and the core rules easily incorporate extras to help the heroes. That feature is probably what made it successful when I ran it for 2 and when I played it with 1 other player and 1 GM--several different genres & games. Try it free:
http://www.peginc.com/freebies/SWcore/TD06.pdf
Next is
Gamma World d20. It is a brilliant & concise adaptation of the D&D 3e rules to the classic Gamma World setting. It's a steal for under $5 for a pdf:
http://paizo.com/products/btpy7zeq?Dungeon-Issue-94-with-Polyhedron-153
Actually,
d20 is a good game for a smaller group without the magic. See above. I ran & played in a few other d20 games with 2 players & 1 GM with good success. A big benefit is that if everyone knows the d20 rules, then it is easy to take what you want & leave out some things to make the game more manageable for a smaller group of players. I ran a pirate D&D with (essentially) no spellcasters (no "flashy" magic) using the firearms rules from the DMG. The 2 players who lasted played fighters/rogues and had a good time with it.
Another was
Judge Dredd d20. It had a rich development, including 4 adventures that were published. 2 main players went through 2 of those adventures, and it was fun. Judge characters are tough and effective, so it is OK to have fewer of them.
The one in which I played was a
Star Wars Revised (d20) all-jedi game. We played 2 jedi characters each but it worked; probably because they started at a higher level (about 8th as I recall). Sadly, we didn't finish that adventure before something else shiny caught the GM's eye.