Not that I have much experience with scenario PBEMs

but I will give my 2 cents :
It depends on what you want, like,...
Balance :
- Meso America, Rise of Rome, Sengoku
Diplomacy and alliance games :
- Napoleonic
Aeronaval :
- WWII Pacific
Famous modern conflicts
- WWI by Sarevok/Rocoteh and WWII Europe by el Mencey corrected by Rcoutme.
Naval experiences and piracy :
- Age of Discovery
Special settings, atmosphere,...
- Sengoku (!), Mesopotamia, Middle-Ages, Great Armada
Of course some go across these categories : Rise of Rome is good if you enjoy the Roman times, Great Armada (though still in test) is overall balanced,... Then there are lots of scenarios that have never been tested AFAIK in PBEMs, at least by me and about which I could not give advice.
For instance Fall of Rome (that would need some editing).
So it really depends if you want balanced settings or if you prefer to plau using infrequent technics (piracy, aeronaval warfare, trench warfare), if you want short ones or long ones (WWI by Sarevok and Rocoteh looks like it could last for ages if there is no early winner for instance) or if you just want to play in settings you like even if they are not balanced because you want to explore the time, units, tech-tree of the scenario for its flavor but against humans.
Then you also have the number of players. MesoAmerica : 3. Middle-Ages : 8 which can slow down a game a lot.
Remember also it is more diffiult to gather a team when a lot of players are required, when the length of the game is very long, etc... as one of the interests of playing scenarios is actually to think (hope ?) you will see the PBEM through, hence I guess the success of scenario-PBEMs.