Well considering the XBox controller was the most common and easiest to preplan for...

Rouge Legacy (if you try using any controller)
Bard's Tale (button layout was crazy if you didn't, which was annoying)
PixelJunk Shooters

I hesitate to add RingRunners, since mostly other gamepads i tried to play with i ended up with huge number lists rather than useful names of the buttons (1-12), and so easily you'd say 'what was button 5 again?' vs being the X on a PS or 360 controller. Wish i could have played that with the keyboard, but mentally i couldn't bypass my old style of playing from Operation Inner Space...

edit:
Forgot about Costume Quest...

More info needed. Someone claimed that earlier also about e.g. Darksiders, yet it works perfectly on Logitech F310 (in XInput mode).

I think I have the first Dark Souls (Prepare To Die Edition) game, maybe I'll try it later. So what kind of problems should I be facing with F310 in this game, just to know what to look for?

If the issues were reported for the wireless model (Logitech F710), then most probably the same issues will happen also on the wireless XBox360 gamepad. There were some XInput games that were reported to have issues with the wireless gamepads, including Microsoft's own.

I googled for "dark souls" "logitech F310", but the first few discussions I read were user errors, either having the gamepad in DirectInput mode (instead of XInput mode), or accidentally having pressed the "mode" button that switches the D-pad and analog stick controls. Some of the discussions became a bit convoluted as well, when other participants started discussing about their own controller problems with older DirectInput-only gamepads.

The third case was more meaningful, which was about the game becoming confused if there were several "(virtual) HID compliant game controllers" listed in Control Panel. Disabling the extra ones apparently fixed the issues. Not sure if that was a Logitech F310 specific problem either, or if it had occurred just as well on XBox gamepad.

I'm yet to test it myself, still at work...

Does the XInput issue even apply to OS X/Linux versions? It looks like [url=http://pingus.seul.org/~grumbel/xboxdrv/]xboxdrv[/url] might do something like this for Linux but again I don't know if this is even applicable as it's not something I've tested.

Yes, Xboxdrv does support xinput and directinput devices, but it's still a hassle to set up properly, if anyone knows a gui for it, please let me know. If someone wants to write a gui for it, I'd even donate something.

As promised, I downloaded&installed&played Dark Souls (Prepare To Die Edition). I played it for about maybe 30-40 minutes until hitting a dead end (no idea what to do or where to go next), and I couldn't see any problem using Logitech F310 gamepad with the game (in XInput mode). At least all the moves mentioned by the tutorials (the readme notes scattered around) seemed to work just as intended. Works fine out of the box, as far as I can tell.

So I think the remark about the game failing to work with Logitech XInput gamepads can be removed. Unless you have some more info about that that I should still try.

Not sure about Dark Souls 2, I don't have the game. Googling for it, DS2 does seem to have some controller issues (performing some of the harder moves that are very tightly timed), but some people reported similar issues even with a real XBox360 gamepad. As far as I could understand, the problem was that the game was running in too high framerate which made the controls harder, so the fix suggested by many for those controller issues was to limit the framerate to 30 fps. Not sure if those issues have been fixed since.

I saw some suggestions that the analog stick deadzone settings of Logitech might also contribute to the problem, but anyway the fix seemed to be limiting the framerate (for either Logitech or XBox gamepad issues). Alternatively, some tried to change the deadzone settings. Either way, at least in those cases the game itself seemed to have generic controller issues, I don't consider it as a case where only the XBox gamepad works fine.

Thanks for testing, I've corrected the entry.

On Linux there are two drivers, the kernel driver (xpad.ko), and the userspace driver (xboxdrv). The kernel driver gets loaded per default, but isn't very configurable. It's pretty much like XInput in that it just describes a x360 controller and thats all there is to it. It didn't use to support rumble, but it does now. Everything that I had lying around that seems to be meant for a x360 pad (with onscreen hints etc) seemed to work with it just fine.

xboxdrv is more like the third party software that you use on Windows to provide an XInput device when you have some other pad, and I think it works for that purpose too. It's most handy when the game doesn't have native gamepad support, since it can produce joystick, keyboard and mouse events. You have to unload the xpad.ko driver to use this.

Unfortunately it's a pain to configure, I'm not aware of any tools for this. I always just wrote a game-specific .ini-style file by hand. Even more unfortunately, in its default configuration or even with the --mimic-xpad switch it doesn't present itself exactly like the xpad.ko driver and I recall at least some frustration when games would expect one of these drivers and work all wonky with the other. But since everything seemed to work fine with xpad.ko now and xboxdrv is at least configurable, maybe this is no longer an issue.

Several further complications occur if you want to use the pad with a game through wine, as the games won't see it like they would on Windows. I've used xboxdrv+x360ce just to play an XInput game with a real x360 controller, and it wasn't exactly straight-forward to configure.

I hate it when a game can be played on PC with a keyboard+mouse setup, but then it displays all of its QTE prompts in terms of a controller layout. Being told to press X, Y, A or B and having to memorise their keyboard equivalents is frustrating.

Stumbled ober another one while defeating my backlog and added Dust: An Elysian Tail.

Added Apotheon and Limbo.
Gosh... I hate having to set up a QJoypad profile for every game.
"Dustforce" was one of the few I tried in the last time that had proper gamepad support.