A quick search gave at least the following possibilities (most of them are not active routes)
LH666 Lufthansa SJO to FRA
AY666 Finnair CPH to HEL
BA666 BA LHR to CHQ
AF666 Air France CDG to LIS (cargo)
UA666 United DEN to TUS
AA666 American Airlines FLL to DCA
RYR666 Ryanair VIE to MBX, interestingly also DUB to BHX
SK666 SAS NYC to OSL
QF666 Qantas ADL to BNE
TK666 Turkish Airlines NSI to ISL
AI666 Air India BOM to DEL
And much more, too much to list everything.