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.
I have a friend from Australia who some years ago wanted to visit Israel and Russia on the same trip. So they did a transfer at TLV. SO it does happen. But I would expect that it is not a hugely common thing. But even so I would expect that a bunch of folks do it every day.