There is likely more because I filter my stuff but here are some entries that really should have the [Program] tag but are missing them.
AceKard 2 (World) (v2.1) (Unl)
AceKard 2i (World) (Unl)
AceKard R.P.G. (World) (Unl)
Action Replay DS (World) (v1.02) (Unl)
Cartridge Construction Kit (World) (v1.22) (Unl)
CodeBreaker DS Lite (World) (Unl)
CycloDS Evolution (World) (v1.1) (Unl)
Data Max (World) (Unl)
DSTT (World) (Unl)
DSTTi (World) (Unl)
EDGE (World) (Unl)
EZ-Flash V (World) (Unl)
EZ-Flash Vi (World) (Unl)
G6DS Real (World) (Unl)
iTouch DS (World) (Unl)
M3DS Real (World) (Unl)
M3DS Simply & R4DS (World) (Unl)
Max Media Launcher (World) (Unl)
Max Media Player (World) (v1.22) (Unl)
Nintendo DS Browser (USA, Europe) (En,Fr,De,Es,It)
Nintendo Zone Wireless Distribution Box DS Card (World) (Rev 1)
Passcard 3 (World) (v6.0) (Unl)
R4i Ultra (World) (Unl)
Relay Station (USA)
Super Key (World) (v6.0) (Unl)
SuperCard DSONE (SDHC) (World) (Unl)
SuperCard DSTWO (World) (Unl)
Edit: And for DSi Digital
Nintendo Fan Network (USA) (Rev 1)
Nintendo DSi Sound (USA) (Rev 2)
Nintendo DSi Shop (USA) (Rev 12)
Nintendo DSi Metronome (USA)
Nintendo DSi Camera (USA) (Rev 4)
Nintendo DSi Browser (USA) (Rev 3)
Nintendo DSi + Internet (USA) (Pre-install)
Nintendo DSi - Instrument Tuner (USA)
Nintendo Countdown Calendar (USA)
Nintendo 3DS Transfer Tool (USA) (Rev 1)