cards I'm missing so far:

-----not in game:
LON-EN102 Spirit Elimination
PGD-EN037 Secret Pass to the Treasures
FET-EN050 Pole Position (OCG and TCG)
LOD-EN100 Injection Fairy Lily (OCG original art)
CRV-EN003 Mad Lobster (OCG art)
EEN-EN054 Weed Out (OCG art)
PP11-JP002 Shuttleroid
YAP1-JP006 Dark Magician Girl (4th art) (TCG art; not in US/Europe versions)

-----sets:
DREV-EN086 Guts of Steel

STBL-EN088 Karakuri Barrel mdl 96 ''Shinkuro''

STOR-EN042 Karakuri Steel Shogun mdl 00X ''Bureido''
STOR-EN052 Karakuri Cash Cache
STOR-EN079 Tiki Curse
STOR-EN080 Tiki Soul

EXVC-EN030 Karakuri Komachi mdl 224 ''Ninishi''
EXVC-EN079 Localized Tornado

GENF-EN007 Drill Barnacle

PHSW-EN027 Telepon D.D.


-----TCG arts:
ABPF-EN045 Cards of Consonance (TCG)
ABPF-EN069 Destruct Potion (TCG)

TSHD-EN013 Infernity Randomizer (TCG)
TSHD-EN015 Infernity Avenger (TCG)
TSHD-EN020 Fairy Archer (TCG)
TSHD-EN049 Into the Void (TCG)
TSHD-EN073 Assault Spirits (TCG)
TSHD-EN076 Power Break (TCG)

DREV-EN032 Amazoness Queen (TCG)
DREV-EN067 Reanimation Wave (TCG)
DREV-EN073 Queen's Pawn (TCG)

STBL-EN061 Heat Wave (TCG)
STBL-EN072 Karakuri Klock (TCG)
STBL-EN076 Vanity's Emptiness (TCG)
STBL-EN079 Tyrant's Temper (TCG)

STOR-EN002 Doppelwarrior (TCG)
STOR-EN014 Ljosalf of the Nordic Alfar (TCG)
STOR-EN015 Svartalf of the Nordic Alfar (TCG)
STOR-EN016 Dverg of the Nordic Alfar (TCG)
STOR-EN057 Token Sundae (TCG)
STOR-EN058 Foolish Return (TCG)
STOR-EN078 Tyrant's Tirade (TCG)

EXVC-EN037 Junk Berserker (TCG)
EXVC-EN045 Scarlet Security (TCG)
EXVC-EN075 Tyrant's Tantrum (TCG)

GENF-EN009 Crashbug X (TCG)
GENF-EN010 Crashbug Y (TCG)
GENF-EN011 Crashbug Z (TCG)
GENF-EN018 Spearfish Soldier (TCG)
GENF-EN063 Asleep at the Switch (TCG)
GENF-EN076 Curse of the Circle (TCG)
GENF-EN077 Tyrant's Tummyache (TCG)
GENF-EN078 Attention! (TCG)

PHSW-EN051 Photon Lead (TCG)
PHSW-EN076 Tyrant's Desperation (TCG)

DDY2-JP002 Backup Warrior (TCG) - unknown if there is a TCG art
JF11-JP007 Buten (TCG)
PP13-JP002 Fallen Angel of Roses (TCG)- unknown if there is a TCG art
PP13-JP003 Machina Cannon (TCG) - unknown if there is a TCG art

anime - Bond Between Teacher and Student (TCG) (not released outside of Japan yet, presumed to have an edit)
anime - Chain Close (TCG) - unknown if there is a TCG art
anime - Destroyed Future (OCG) (not released outside of Japan yet, presumed to have an edit)