I'm debating whether or not it's worth spending the money on the wiiware version and was wondering if anybody had any input.

From what I've played, the Wiiware version is undoubtedly superior to the free pc version.

I think they're the same gameplay wise whereas the Wii version has enhanced graphics so it looks a little snazzier. If you're low on funds then you should download the free PC version otherwise you might as well support them and buy it.

The Wiiware version is pretty amazing. Although, that game gets balls hard nearing the end.

The PC version, which is free, has mods.  This is makes it superior in my view

@L0ki:

The WiiWare game is awesome, it's only 1,000 Nintendo Points and you could have no complaints about it's quality, however, I should point that Cave Story 3D for 3DS is going to be released later this year, on August 9th, and that looks to be the best version yet. It will be priced as any other 3DS game though.

  

  

   

I bought the new 3ds eshop version for 10 bucks. It is my first playing the game and I am really liking the story and challenge (though forgetting to save and having to restart from WAAAAY back sucks) The new 3d effects are subtle, but great on the pixel artsy backgrounds.