In the airport in Tel Aviv (Ben Guirion) I noticed a sign for "international transfer passengers". This piqued my curiosity... is there actually a "city pair" (with both cities outside of Israel) where it would make practical sense to change planes in Tel Aviv? I can't think of any pair like that.
Because of the lack of diplomatic relations with so many countries to the East, El Al has a very limited number of flights that go Eastbound from Tel Aviv, and most of those flights (Beijing, Bangkok) take very circuitous routes to avoid flying over countries which are technically at war with Israel including Iran, Iraq, Afghanistan, etc. So if you were going East-West, Tel Aviv is almost never the best place to do it.
That means that the number of possibilities to use El Al and connect in Tel Aviv is miniscule, and although there IS an international transit route through Ben Gurion airport, I've never seen anyone use it.
One possible use would be for tourists who wish to visit a combination of Israel and Jordan. They might connect through TLV on their way to Amman, for example, then go overland back to Israel, and fly home through TLV.
Geographically, it might make sense if you are travelling from Johannesburg to St. Petersburg; there don't appear to be any direct flights between those two cities, yet they are both serviced by El Al (with a transfer in Tel Aviv).
Well all airlines have a home hub out of which they operate, and sometimes other hubs.
This means that it's very common to fly between two cities on the same airline via one of these hubs.
If you don't understand why anybody would want to fly via a hub rather than a direct flight, there are many reasons including frequent flier points and cheaper tickets.
So my answer is any two cities serviced by El Al would be such city pairs, and quite possibly other airlines too.
As others have noted, it might make sense going North/South.
I recently travelled from Johannesburg to Bucharest via Israel. I think it probably was a relatively cheap way to make the trip - first leg with El Al, second leg with Wizz Air - but I wouldn't necessarily recommend it: El Al is pretty bad, and it was a pain to 1) get subjected to 40 min questioning in Johannesburg airport before getting on the flight to Israel (maybe less likely if you're not a man travelling alone) 2) have to transfer terminals and go through security again at Ben Gurion.
(FYI, my trip wasn't as a result of finding the cheapest or most convenient flights - it was because I already had a return flight to Israel booked from Johannesburg and then moved the outbound flight one week earlier to get a work trip to Bucharest in.)