I believe below list should be correct. The keys which are no longer in use, became useless - they cannot open doors they used to open - so I understand it as a change of it's role.
Key 0000 - Rumours says it once opened every door in Tibia.
Key 0004 - An old Thais city alpha key. This key is no longer in use.
Key 0005 - An old Thais city alpha key. Key used to open the door to Daemon first demon in Tibia. Only a couple are known to exist 3 in Antica 1 on Libera other key unknown due to transfers. Owner on Antica may be Bubble, Nietz, and Tharanic
Key 0006 - Bridgekeepers house. This key is no longer in use.
Key 0007 - An old Thais city alpha key. This key is no longer in use.
Key 0009 - An old Thais city alpha key. This key is no longer in use.
Key 0020 - Thais Jail key. This key is no longer in use.
Key 0021 - Thais South Gate Guardhouse. This key is no longer in use.
Key 3100 - Old Skjaar key.
Key 3900 - Old guild hall key. This key is no longer in use.
Key 3901 - Old guild hall key. This key is no longer in use.
Key 3902 - Opened Opa Wetterwachs Tower.
Key 3909 - Old guild hall key. This key is no longer in use.
Key 3910 - Old guild hall key. This key is no longer in use.
Key 3911 - Old guild hall key. This key is no longer in use.
Key 3912 - Old guild hall key. This key is no longer in use.
Key 3913 - Old guild hall key. This key is no longer in use.
Key 3914 - Old guild hall key. This key is no longer in use.
Key 3915 - Old guild hall key. This key is no longer in use.
Key 3916 - Old guild hall key. This key is no longer in use.
Key 3917 - Old guild hall key. This key is no longer in use.
Key 3923 - Old guild hall key.
Key 3925 - Old guild hall key.
Key 3930 - Mercenary Tower key. Comes in wooden and copper variants. This key is no longer in use.
Key 3931 - Mercenary Tower key. This key is no longer in use.
Key 3932 - Mercenary Tower key. This key is no longer in use.
Key 3933 - Mercenary Tower key. This key is no longer in use.
Key 3934 - Mercenary Tower key. This key is no longer in use.
Key 3935 - Mercenary Tower key. This key is no longer in use.
Key 3936 - Mercenary Tower key. This key is no longer in use.
Key 3937 - Mercenary Tower key. This key is no longer in use.
Key 3938 - Mercenary Tower key. This key is no longer in use.
Key 3950 - Old Cyclops area in Fibula. This key is no longer in use.
Key 3960 - Opened the Flute Room in Fibula. Comes in wooden and bone variants. This key is no longer in use.
Key 3970 - Old Fibula key. This key is no longer in use.
Key 3988 - Old guild hall key. This key is no longer in use.
Key 4210 - Old guild hall key. This key is no longer in use.
Key 4600 - Training Room in the Rookgaard Academy. This key is no longer in use.
Key 5002 - Used to open a door in the Black Knight's Villa. This key is no longer in use.
Source: https://tibia.fandom.com/wiki/Keys