It'd suprise me if EMM386.EXE not being loaded in config.sys is causing Windows to not boot, unless this is Win3.1. (You mention Safe Mode won't load either, which means it's DEFINITLEY not the lack of emm386 in config.sys, as safe mode doesn't even touch config.sys).
Now, if you outright deleted the actual emm386.exe file, what you're probably going to have to do is extract it manually from the Windows CD.
Here's a (partially inaccurate) document on it at Microsoft's support site.
http://support.microsoft.com/suppor...nk=2&src=DHCS_MSPSS_gn_SRCH&SPR=MSALL
The example command line reads EXTRACT A/ D:\WIN95\WIN95_02.CAB ENABLE3.DLL C:\WINDOWS\TEMP
It should be EXTRACT /A D:\WIN95\WIN95_02.CAB ENABLE3.DLL /L C:\WINDOWS\TEMP
Although you won't want to extract to C:\Windows\temp
Here are the commands for the different versions of Windows:
Win95(any version): extract /a D:\win95\win95_02.cab emm386.exe /L C:\windows
Win98(any version): extract /a D:\win98\win98_22.cab emm386.exe /L C:\windows
WinME: Unknown.