This is a comprehensive list of the best total conversions for DOOM. The only one I think they are missing is the Alien TC. I know the link says they are for GP32, but they work on any system.
Classic DOOM in DOOM 3
Those crazy modders recreated DOOM 1 for the DOOM 3 engine. All you need is the demo and a high end computer to play this.
Large disc support for Windows 98 for more than 137 GB
This is an odd find. Now there is a patch for Win98 that allows large disk support up to 2 TB. Your motherboard bios must support large discs for this to work.
NTFS for DOS
This program allows read and write access to NTFS partitions in a DOS environment. This is a wonderful tool for system recovery. This is from the same guy who exposed the Sony audio CD rootkit.