I misread the OP so my whole answer doesn't make sense. I thought it's asking about maps with most games ever created on them. I don't want to delete all I wrote so here it is:
1. Modified Medium Earth
2. Small Earth Board Map
3. Rise of Rome
4. Duel
5. Imperium Romanum
6. Europe
7. Medium Earth
8. Small Earth
9. Final Earth
10. Europe Huge
11. Scrabble
The most "popular" ones are obviously going to be the ones featured in:
- ladders (which is originally ME, and nowadays MME/FE/Europe; RT Ladder was a thing for a bit too)
- QM, especially the templates unlocked first (SEBM and MME again; Four Castles is a rare game, and I've never seen the Siege map outside QM)
- auto-coin games (historically used to be SE and MME most commonly; btw, Small Earth Board Map is actually a new-ish addition, I don't remember when exactly did it replace the original SE map)
- auto-games (again ME/MME)
- lotteries (we all know that one)
and those that are especially common in open games (ROR/IR I think take the cake, I also feel like I've been seeing Europe Huge especially often, as well as various GOT maps but the numbers might be too splintered between them)
Some consideration could be given to maps especially popular in the strat community throughout the years (which is ME again, MME again, Europe again, maybe IR again), however it's hard to say how much can it "skew" the results. There's also the diplo community which I haven't been following in six years now so I don't know if there's something that they play especially often.