If you want to remain in control of your computer (instead of your computer being in control of you) a prerequisite is to use only open source software. Hence you most probably want to run GNU/Linux. Nowadays there are plenty of distributions available in one click of the mouse. However, purists may never be fully satisfied with any of today's standard distributions: too many unnecessary programs, cumbersome package managers, a lot of disk space wasted by GUIs…
If you want full satisfaction from your Linux box and a thorough understanding of what every component does, of why and where the bits get installed, if you do not want to burden your computer with programs that you will never use (such programs should definitely not be installed since only a cracker might find them useful), then you have to compile your own system from scratch, using only the source code. A custom-built system is easily obtained by following the detailed instructions of the Linux From Scratch (and Beyond) project:
I have put together some scripts
that automate the process
of compiling together a complete Linux system from source code: following LFS-6.0 instructions, these
yield a fully functional no-frills operating system using 600M of disk space
(which include 280M of kernel sources).
Feel free to use them, adjust them to your needs
and let me know of any problems encountered.