You're missing the point. The OP wasn't talking about the size or obscurity of the city, s/he was talking about "unexplainable/weird nonstop city pairs" (in other words the route, not the cities) for a particular airline.
CX BKK-BOM or DXB-BOM (don't think this one operates anymore...) are strange because neither are a CX hub (though, now that I look, it seems BKK has morphed into a mini-hub for CX; they also service DEL, KHI, SIN, and CMB from BKK). Ditto with SQ TPE-LAX, SQ FRA-NYC, or MH JFK-STO (not seeing this flight anymore either).
Here are a few of my own (I've bolded the ones I knew about off the top of my head and the rest are from poking around
ARM):
SQ IAH-DME (this one takes the cake, IMHO; I actually put a bunch of adoptive parents on this flight, very nice flight, but it's very strange to be flying on Singapore Airlines from Texas to Moscow)
SQ SFO-ICN, SFO-HKG
SQ AUH-KWI, AUH-JED, DXB-IST,
DXB-CAI, DXB-RUH
SQ MXP-BCN
SQ JNB-CPT
MH LAX-ICN
MH DXB-BEY, DXB-DMM
QF BKK-LHR, HKG-LHR, SIN-FRA, SIN-LHR, SIN-BOM
MS BKK-CAN
RJ BKK-HKG, BKK-KUL
AF MIA-PAP (actually a pretty sweet flight; I especially utilized this after the Haiti earthquake to get aid workers down there; they have dirt-cheap prices on the MIA-PAP portion, too), PAP-PTP, FDF-PTP, FDF-CAY, FDF-SDQ, PTP-SDQ, SDQ-PUJ
Just plain strange:
EI MAD-IAD (this is a strange one that is operated by EI, but coded as UA subsidiary (not code share)--EI doesn't sell it, except as a "double-code share" back from UA. I'm guessing it's something akin to a
wet lease. I'd be very curious to know if it has EI or UA livery and whether it's EI or UA employees; I suspect both are EI, but the flight description says to check in with UA. Weird.)
I know there're more that I'm not thinking of right now...