, i am not 100% certain what you mean. you can make linux (the kernel) from sourcecode if you wish, then a few other things so you get base system, rest you can add as you see fit.
if i am not all wrong you should even be able to do it with knoppix as startingpoint.
here you have a link for Linux From Scratch (LFS), http://www.linuxfromscratch.org/
in their own words.
LFS is a project that provides you with step-by-step instructions for building your own custom Linux system, entirely from source code.
if you just want to make your own programs for Linux, just go ahead.
the tools (compiler, debugger...), kernel-header, libraries... are already included in most distributions. you can use C, distC, C++, fortran77 and many other languages.
here you have a few howtos on linux in general, some have conections to programing.
http://www.ibiblio.org/pub/Linux/docs/
here are most of the programing related ones in one page.
http://www.tldp.org/HOWTO/HOWTO-INDEX/programming.html
have a great time with linux