Hi Joseph,
I use Vutrax for PCB design (a commercial program dating back to DOS days but still updated for Windows and Linux). gerbv for gerber viewing.
emacs for text editing, could look at Eclipse if you want that type of environment.
Various gcc toolchains for embedded/microcontroller programming (mainly ARM7 and cortex-m3 code now, but also AVR and C167 in the past). I also use it to cross-compile some simple windows utilities, mainly firmware updaters so my customers can update products.
openocd for JTAG flashing/debug, and the gdb/insight graphical debugger.
git for revision control (all types of file, not just programming).
Inkscape for vector graphic editing ("graphic design"). Like front panel overlays and illustrations for manuals. Also great for extracting graphics from existing PDFs.
The gimp for the bitmapped formats, photo editing, screenshots.
Firefox browser, thunderbird for mail.
emacs again for usenet.
LTSpice under wine (works well, need the xchm help viewer to read the help file).
Python and "Linux GPIB" drivers for writing instrument control programs.
Openoffice for word processing, spreadsheets etc. Will switch to the LibreOffice fork if reinstalling. Also TeX (actually the Context variant/macrolanguage).
VirtualBox and dosbox for virtualization as mentioned. I would look (again) at kvm/qemu if starting anew, now VirtualBox is controlled by Oracle. But VirtualBox is still very good at present.
There are dozens of others, xpdf, ImageMagick, vnc, f-spot, gtkam, all the KDE stuff, ssh, the various servers.
They all update themselves automatically (except the toolchains I compiled myself). A single update tool handles everything in a unified way, even running software can be updated without reboots etc.
Regarding the distribution, it has been debian since 2001 (just checked!), The same original install keeping itself up to date for the last 11 years, migrating from machine to machine as I upgrade hardware. Current version is debian "squeeze". I would consider the debian-derived Kubuntu for a new install, using it on a laptop and looks good.