The four bomb passwords are necessary for the final ending. All of them are English phrases, encoded by being shifted back one letter in the alphatet.
Bomb 00: LXA QNS GDQ (encodes MY BROTHER)
Bomb 01: BQZ RGJ DXR (encodes CRASH KEYS)
Bomb 02: EQD DYR NTK (encodes FREE Z SOUL)
Bomb 03 (on US/European version): LXQ LHC NMR (encodes MYRMIDONS)
Bomb 03 (on Japanese version): BKZ XCN KKR (encodes CLAYDOLLS)
MY BROTHER is the name of the leader of the terrorists.
CRASH KEYS is the name of the organization that Akane Kurashiki works for. It may also be a corruption of Kurashikis.
FREE Z SOUL is a corruption of "Free The Soul", the name of the conspiracy.
MYRMIDONS or CLAYDOLLS is the name given to the terrorist operatives (the name is different in the English and Japanese versions, so the password differs too - although if you set the English version to Japanese audio, you can still hear the characters refer to "Clay Dolls", which is an homophone for "Cradle", in Japanese.)
ID: GTFDML016 (JPN-Version: GLTFTM016), Password: MILKEVOLI
The English ID, GTF-DM-L-016, is Luna's GAULEM ID, which stands for "GAULEM Type Female - Diana Model - Luna - 016 (most likely because 016 is dio backwards). However, it is confirmed that the Japanese version of the ID is incorrect and was supposed to be just like the English ID.
The password, MILKEVOLI, is "I love Klim" backwards. Either this is a reference to how Luna is one of Sigma's creation or how Luna is modelled out of Diana.
Username: KURASHIKI, Password (US/Euro version): JUMPYDOLL, Password (Japanese version): GRAPEDOLL
The english password, Jumpydoll, is a reference to the doll presented to Junpei during the credits of 999, back in the past after Akane had been rescued. It's also a reference to the nickname she had given him, "Jumpy".