There is a tool from microsoft for emulating a DOS (16 bit) environment for older games - this includes an emulated ISA sound blaster 16 (which is the sound card that EVERY dos game back then used!)
It is called VDMS, you can get info and links/downloads from
here.
I think what you are refering to by giving you the option to choose a game at startup is some kind of DOS program that loads before windows? There is not much point in using those anymore because of lack of DOS drivers, compatible sound/video cards and incompatibility with Windows XP. I believe that they used the instance of DOS that windows 3.1/1, 95, 98 or ME was using to boot and the program would be entered in Windows' Autoexec.exe file to open.
When it comes to running DOS games that required a CD they would usually only allow you to use drive D. If you use different hard drive partitions causing your CD drive to be something much higher up in the alphabet then you can just copy the contents of that CD to the partition D.
I hope this helped a bit.
(and looking at that list above, the original Doom rocks!)
