Sorry to bring up an old thread.
Firstly I'd like to ask how the Linux port is going? it seems the discussion died down about it somewhat.
I'm wondering how you guys are handling the OSX port in terms of case sensitivity. I don't really know why this hasn't been posted in this thread, but OSX's file system is also case sensitive (as are all the ones I've heard about apart from the Windows ones). OSX is based on BSD and hence is Unix-like, much like Linux. Both OSs use file systems which are case sensitive. Maybe the old HFS filesystem wasn't, HFS+ and the upcoming ZFS filesystem are case sensitive, so you would be running into identical problems as you are with Linux. I don't like how Linux is being blamed for that.
Also it's quite probable that, given that Windows will ditch backwards compatibility, Vienna (or whatever the next Windows will be called) will also feature a case sensitive FS since it's the logical thing to do.
Having skimmed over the
Comparison of File Systems wiki entry I noticed NTFS is case-sensitive as well... so aren't you having problems either way? I might be being ignorant since such a thing would be hard to miss...
I'd also like to say that I am interested in the port. I won't say that I will buy the game, as I don't know if I would want to play it (irrespective of platform), but if I were to buy it I would only do so if it was a Linux port since that is my OS of choice.
I don't know about others but being a Linux user I tend to look at quality over branding/flashy graphics (not that Aquaria doesn't look great). Windows users may not see this as a great game because I think Windows users tend to look more at the graphics and how mainstream the product is, so selling it in that market may not be too great. The whole concept of having a 2d side-scroller is pretty much considered to be "old" and people don't like "old" stuff.
There is definitely a small market on the Linux platform, but it's a tricky issue. As someone has already mentioned it's a "Catch 22" scenario. You can't really buy anything that doesn't exist, so you can't accurately say how big the Linux market is. There are a lot of great games on Linux, a lot of them are open source, but most (apart from the commercial ones) tend to look old. I don't know why... either way there aren't many games that are attractive to a typical Windows user. There are games like the Quake, Doom and UT series as well as some other mainstream games but that's about it. People don't want to game on Linux because it lacks the big titles that are on Windows. Because of this companies also don't see any profit in Linux, and the circle closes, Linux is left without any major titles to bring in more users. There's also the issue of DirectX which locks in developers to the Windows platform, but luckily it does not apply for Aquaria.
It is early days for Linux, and gaming hasn't really been born yet. Linux (and *BSD and even OS X and similar) needs companies, or indies, to develop games so as to create the possibility of a market. Linux will most definitely grow, but it will grow faster if (good) games are available on it.
I'm not really targeting that at you, I'm just describing how I view the whole issue of gaming on Linux. I see that the port is going well, and hope that you do get there. It would be great to have a cool and original game like Aquaria on Linux and hopefully you will be part of the developer community that paths the future of Linux gaming
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. Not sure if I'd buy the game in that scenario though, it all depends on how great it is I suppose 
. Out of respect and having seen the native port attempt I won't be pirating it. It's a shame to see 
It crashes at the loading screen. Oh well, off to Windows we go.