I'm not sure what is meant by "VPN", but the other two are vastly different.
Bochs and Qemu will emulate a CPU architecture, like x86. You'd most likely need this if you wanted to run something closed-source on Linux, since most commercial Linux software is compiled for x86 and not ARM (Cortex A8). It would be dog-slow doing this on a mobile device.
If you're just wanting the OS and open source software (KDE, Firefox, etc.), you'd be better off setting up a chroot. The software in this case would be communicating directly to the same Linux kernel that's running Android, so it would be much faster. It would limit you to using that kernel as well, which may or may not be a problem for your project. You'll need a distribution that is compatible with your CPU. I believe there's a Debian branch for ARM.
p.s. When I say "commercial Linux software", I should probably specify I meant commercial software compatible with GNU/Linux, because Android apps are also Linux software. Linux is the kernel. GNU or Android is the rest of the OS. Praise be to RMS and all that.