TheChuckster, WinterMute, Jefklak has updated DS Doom, a port based on PrBoom, and now supports DLDI. Do also note that they have moved to a new website.
From the official site:
(Apologies if this is old news, it is new to me! I tested the M3 Simply and visuals and sound works at speeds one would expect doom to run at.)
From the official site:
Official Site with downloadQUOTE said:1.1.0 Rev1: (04 Jan. 2007)
 1. Added save support for EZ-Flash IV, Ewin2, G6 Flash, MaxMedia, M3, ... cartridges via Chism's Dynamically Linked Device Interface (DLDI). Thanks to Scrawl! (The binary and source download files have been updated). You will need to patch the binary with the appropriate DLDI patch (download and explanation all found here) before it will work!
(Apologies if this is old news, it is new to me! I tested the M3 Simply and visuals and sound works at speeds one would expect doom to run at.)