Hi D.C.
First a question:
When you say "I have a Operating System installation disk that does not boot on startup." Have you ever been able to boot from CD or only from floppy or hard disk. If you have never been able to boot from CD even when using commercial operating system diskettes, then the problem lies in your BIOS or in the CD-ROM. The bios must support booting from CD and the CD-ROM must be ATAPI compliant to use as a boot device.
As to the rest of your question: the files needed at boot up depend on the operating system you are using. For example: basic DOS functions are handled by hidden files IO.SYS and MSDOS.SYS which call the non-hidden files COMMAND.COM and CONFIG.SYS and AUTOEXEC.BAT . You can get the basic functionality by making a boot floppy using FORMAT A: /s and then using ATTRIB to unhide IO.SYS and MSDOS.SYS and then copying the whole contents of the floppy to the cd project.
That is for DOS, Windows 9x uses IO.SYS and MSDOS.SYS as the hidden files andalso requires CONFIG.SYS, COMMAND.COM, AUTOEXEC.BAT. Additionally, you need WIN.COM, KERNEL32.DLL, KERNEL386.EXE, GDI.EXE, GDI32.EXE. If you want to provide backward compatibility for 16 apps you need WIN.INI, WINFILE.INI and SYSTEM.INI. Windows 9x also requires registry files found in the /Windows directory. These are USER.DAT and SYSTEM.DAT.
This should get you started. As a note, some of these files are hidden system files, and to see them in windows explorer you need to click Tools, Folder Options, View and then select "Show hidden files" and deselect "hide system files". Then you can see all of the needed system files.
I didn't include steps for NT or Windows 2000, I hope that instructions for DOS and Windows 9x should fit the bill. Let me know in a rating reply if you need more help.
Cheers,
dan