I haven't heard of any fully universal (as in within a single generation working with PC, Sony, MS, and Nintendo systems out of the box, except maybe the i-pac, which I'll get to in a bit). Like Dirty Hipsters has said, either go with the PS360/PC ones or wait it out a few more months and see if someone makes a PC/PS4/Xbone/Wii U stick. All I can say for sure is buy something with real arcade parts, like Sanwa or Happ, in it. The x-arcade stuff is decent, but I hear the sticks can be funky. (To this day, I don't know what brand of parts they use.)
Another couple options requires you to get dirty (and I regret thinking about them because now I want to try them). So read on only if you might be interested or like reading build log type stuff.
You could get a cheap and/or broke stick off Ebay (or your preferred location for cheap stuff). (Make sure it's the electronics, not the joystick itself, that broke. Otherwise you gotta buy that, too. Buttons are cheap and easy to replace, so if a plunger or micro-switch is bad, the unit is probably still worth it.)(Or make the entire stick yourself. There's plenty of tutorials online on the best layouts and how to do all the under-the-hood work.)
Then grab some sacrificial controllers for whatever system your planning on using it with. Bypass all the buttons and d-pad directions on them by soldering those contacts to the corresponding points on the arcade stick's switches. You can either use big connectors with many poles and plug in the appropriate controller when needed or try to stuff it all into the box. (Also, if you're really neat and tidy, you might be able to cut a hole in the plastic controller case, feed the wires through that, use the plugs, and use the controller normally when you'd like.) With this way, you can do any system you want, and, to get PC/Wii U/360/PS3/PS4 compatibility, you only need a Wii U pro pad, a 360 pad, and a PS3 pad. Substitute the 360 pad with a xbone one or add it if you want. This gets more expensive if you want a two player setup. But the good thing is you can either use controllers with broken analog sticks or try the "plug in" method to keep costs down.
If you had the room to hide everything and want to get really fancy, wire them up so each controller has a switch to cut battery power. Or, find out if the pad you're modding uses a common ground for the buttons and put a switch in there to cut its input when you're using a different system.
The other option is to get an old stick/make one like above, then get an i-pac or other arcade controller board. I know i-pac has PC functionality out of the box and you can buy adapters for xbox(the first one), 360, PS2, PS3 and Gamecube (along with any Wii or Wii U games that support GC pads). It's not very cheap, compared to a stock PC/PS3/360 stick, to get an i-pac, the joystick(s), buttons, and whatever adapters you want, but I thought I'd throw that out there for anyone else reading my wall of text.