Some programs (especially oneworld) require minimum segments on the own metal. So it may be difficult to fly on those airlines.
The big question is: Do you prefer status or award flights.
Be aware that earning and spending is different on each program.
The best program depends on, your flying pattern, booking classes, airlines and location.
Some programs offer Lifetime Status, so they are quite interesting in the long run.
My best programs.
For Status:
AB: Air Berlin, German Credit Card (needs German bank Account) gives status miles.
Status benefits on Oneworld and
Etihad Partners (so Virgin and Qantas).
50K Statusmiles
Negative: Bad financial situation.
If you travel in premium cabins QF and BA are quite good to get a status.
BA offers al lifetime Emerald, but no lifetime Saphire or Ruby.
For Star Alliance:
Turkish and Aegean are quite interesting. Aegean needs 4 Segments on their metal.
Asiana offers quite an interesting Lifetime Status (Star Gold for 500K Miles).