O.K, now we have a system on top of which you can install X11(Apple has also implemented X11 in Aqua but its highly customized to support Aqua alone, so we install our own X11 and later other X stuff). Once you have that, you
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What's wrong with the X11 bundled by Apple? What do you mean by "customized for Aqua"? I've been able to run all my X11 apps, XFCE included without any trouble on it.
Once you have that why use Aqua and Proprietary Apple Applications and Utilities at all :-)
Because they improve your productivity and generally make things much easier for you, as a developer. I'm not kidding; Xcode bundles a lot of POSIX documentation with it; man pages in HTML format etc etc. No free software has yet been able to match the raw power and ease-of-use that some of the developer tools from Apple give you.
The other option is format the preloaded Mac OS X when you buy an Apple machine and a GNU/Linux distro on it. Then you essentially have a Free Operating system on the Apple hardware, this can be done just as easily on both older PowerPC Mac's and the newer Intel Mac's.
I was indeed running Gentoo Linux natively but it didn't take me long (6 months) to come back to OS X. Part of the reason was that I invested a lot on the Apple hardware but wasn't able to utilize it to the fullest because of the lack of drivers on Linux. The ATi driver that gives you a decent screen to work on was non-free anyway; webcam support was very very buggy and sound was always crackling. Not to mention I had to spend 4 hours in trying to get the in-built microphone to work. Since I have to use non-free software to actually even use my system running Native Linux; why not use OS X?
Also, I can now develop free software for both Mac and Linux; which is awesome. I have a setup where I run Linux in a virtual machine; ssh to it through X11 forwarding and run Linux-Mac apps side by side. This also means that I am free to play around with the kernel as much as I want without fear of screwing up the system. Basically; I'm in a much better position to develop software for Linux by running it on OS X, and wasting minimal time doing it thanks to the awesome, albeit non-free Apple applications (try the debugger bundled with Xcode; it will change your life forever)
My conscience doesn't hurt me when I use non-free tools to create free software. There are also several Free Software built natively for the Mac; and I am now in a position to contribute to them. Short version: I'm loving it :)