From EZ-Flash Wiki
Homebrew for the EZ4 requires you to use ds.gba format. The ds.gba format is the same as .nds save a small GBA header that is attached to the rom. There are a few ways to do this: You can either grab a header and use something like the following MS DOS command line:
copy /b homebrew.nds+header.gba newhomebrew.ds.gba
Naturally you would change the names to match, at this time the best way to get a GBA header is to generate one.
You can also use DSBuild, now it comes as part of the devkitpro tools but 20 megs for a file only a couple of KB is a bit of a time waste so here is a mirror: http://www.4shared.com/file/2228491/ef07d789/dsbuild.html
Alternatively you can try naming the file with a .bin extension.
The EZ4 has a DLDI patch available meaning most new homebrew will work and a lot of other homebrew has been recompiled to use it, there exists a reasonable amount of homebrew built prior to the introduction of DLDI with EZ4 specific compatibility.
For code that uses SRAM to save read the following thread SRAM issues with the EZ4
The following items have all been tested on an EZ4. For games & applications requiring Wifi Mario Kart DS was previously used to set up the wifi connection.
Please note: This information is not to be meant a repository for homebrew development. This is not a news site and updates may not be frequent. It is designed to help users determine which Homebrew game or application will work with the EZ4 carts. Contributions and submissions from other users are appreciated.
A Touch of War - Working. No wifi.
Chaos - Working. A port of a GBA homebrew title.
DSDoom - This DLDI version works perfectly. Patch with EZ4 DLDI driver.
Explosive Gas - Working
FlashbackDS - Working. Use the "flashbackDS.GBA_NDS_FAT.ds.gba" file. You'll also need a copy of the DOS version of Flashback.
HexenDS Working. This homebrew hasn't gamesave yet.
International Karate DS - Working.
MegaETK - Working, however you have to use the "no-fat" version. It cannot save or load.
No Place to Hide - Working. Can lock up after a few minutes of play.
PhotocupDS - Working(use ds.gba version no use of client)
QuakeDS - Works perfectly. You must rename it from .nds to .bin and patch with EZ4 DLDI driver.
Rubberbands - Working. Nice puzzle game.
Tales of Dagur - Working.
Teenage Queen - Working.
Touch me (I'm Famous) - working but hangs sometimes
Twin Isles - Works perfectly, add a save patch with Ez4client.
Warcraft Tower Defense - Works perfectly. Use the FAT version and patch with EZ4 DLDI driver.
Wolfenstein 3D - Works perfectly.
Zelda Platformer - Working, no saving.
AMAP4DS Works. Subway Maps for many countries. Use the *.gba file but change from ".gba" to ".bin".
Beup Live V0.3 - Working. Use No-fat and copy through EZ Client to save login/pwd.
Dissonance - Working (very buggy, application fault, not EZ4)
DSFTP Works perfectly. Patch with EZ4 DLDI driver.
DSLinux Works almost, writing is not supported.
DSLua - Working, GBFS version only.
DS Organize Works perfectly (read&write) now that it has DLDI support. Patch with EZ4 DLDI driver.
DS VNC Not working. Does not support Read/Write access to the miniSD & microSD.(Work with RealVNC server, not with UltraVNC)
ETool Able to grab saves off of real DS carts. EToolSMS tested with an EZ4 and Advance Wars original cart.
FrodoDS This EZ4 version works properly. However, the emulator is very slow.
Goomba - Works Perfectly
Mandelbrot Set - Working.
Moonshell V1.6 stable - Works great.
NDSMail - Working. Settings cannot be saved or loaded, mail / news retrieval works.
NesDS - Working. Use the ds.gba version and patch with EZ4-64.exe to get a 64kb savefile.
Picodrive - Working 1.7 patch with DLDI and ezclient. Save roms to card and run bin to load games.
Reinmoon V0.3 - Not working. Does not support Read/Write access to the miniSD & microSD.
ScummVM DS - Works perfectly with the new DLDI version. Patch with EZ4 DLDI driver.
SlyphIRC Works, not sure if it has save support, keyboard is a bit off, not ez4 fault though.
SylphAmp V0.3 - Works great. Streaming audio via Winamp in crystal clear stereo, who could ask for more ?
TI Calc Emu Black screens with both the 83 and 85 version.
VoiceChatClient 0.1 Works fine. Needs Darkfader's loader prepended to the front.
Win2DS Works pretty good. Its a little slow but it works.