From existing...
Antarctica - ATA (not ART)
Curacao - CUW (not CUR)
Christmas Island - CXR (not CHR)
Falkland Islands - FLK (not FAL)
Faroe Islands - FRO (not FAR) - there is already one FRO flag, but I can't identify the territory
French Guiana - GUF (not FRG)
French Polynesia - PYF (not FRP)
Guadaloupe - GLP (not GDL)
Guernsey - GGY (not GUE)
Isle of Man - IOM (not ISM)
Jersey - JEY (not JRS)
Montserrat - MSR (not MTS)
Tokelau - TKL (not TOK)
Turks and Caicois Islands - TCA (not TCI)
Saint Martin - MAF (not SMI)
Sint Maarten - SXM (not SMA)
Wallis and Futuna - WLF (not WAF)
Western Sahara - ESH (not WSH)
From proposed...
Vatican City - VAT
Bonaire, Saba, Sint Eustatius - all have BES (together called Carribean Netherlands)
Saint Barthelemy - BLM
Saint Pierre et Miquelon - SPM
Cocos (Keeling) Islands - CCK
Saint Helena - SHN
Pitcairn - PCN
British Indian Ocean Territory - IOT
French Southwest Territories - ATF
South Georgia and Sandwich Islands - SGS
Other proposed territories like Bougainville don't have them apparently, so you can use @heywoodu's work I guess.