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You can also try to find a game in one of these GOGmixes:
http://www.gog.com/mix/games_that_love_the_xbox_360_controller
https://secure.gog.com/mix/usb_gamepad_compatibility
Good luck. I hope your nephew enjoys PixelJunk Monsters.
I was going to suggest the LucasArts-era Monkey Island games but I just found out GOG doesn't have these... what the heck?
Stacking.

Just regardez-vous the game page here, highly recommended for a young 'un.

Not sure about controller support, though.
Forgot to mention Beyond Good and Evil. It's a nice game, colorful and not very difficult.
Re-Volt
This is a racing game with remote-controlled race cars, it's pretty nice. It reminds me somewhat of Mario Kart, it's whimsical and you have weapons like water balloons or fireworks rockets. The physics are weird, but they are appropriate for toy cars. You can plug in any HID controller (gamepad, racing wheel) and there is even split screen multiplayer (which is a rarity on PC) if you install the latest unofficial patch. You can also download new user-made race tracks and cars. I don't know how to judge the difficulty, the game kicks my butt, but I'm not good at racing games in general.

Theme Hospital
you manage a hospital and cure silly made up diseases like inflated heads. The game is fairly easy to pick up and increases in difficulty, but it's in English and some other European languages only, I don't know if that might be a problem. It can only be played with mouse and keyboard because it is very much driven by menus and pointing&clicking.

Rollercoaster Tycoon
I'm putting this one up just because it's a nice game as well. Much of what was said about Theme hospital applies here as well, except that you are managing a theme park instead.

Pinball Gold Pack
It's pinball, that's really all there is to it, but it's fun. The game has no controller support, but you only need three keys (left and right flipper and a key to launch the ball), so you could use the built-in DOSBox key mapper or Joy2Key or something similar to map those keys to gamepad buttons.
Post edited December 22, 2013 by HiPhish
I can't believe I forgot this one:

Tyrian 2000
This is one one of the free games you get when signing up on GOG. It's a vertical shmup, it supports gamepad, keyboard and mouse, it has adjustable difficulty, local multiplayer and you can play either the campaign where you beat levels and buy upgrades for your ship, or arcade mode where you pick up upgrades as you go along. Since it's free there is really no reason to get it.