Well there is 2 "popular" payloads out there, PL3 and Hermes (probably very individual liking), i think but not sure that Hermes v4b is the payload with most compitability, i use it and can run i.e AC:Brotherhood.
And same for the managers a lot of people would probably say different ones, me im using latest gaia and afaik its working like a charm, still out there you have some major ones open manager, gaia, multiman, cover manager, rogero well you name it, but i found gaia satisfying for me
FTP apps there is 2, latest (completely legal) PS3 FTP and there is blackbox FTP, to me it seems blackbox is more stable for the moment, but hopefully PS3 FTP will get some fixes as that one is completely legal wich imo is nice
it all comes down to your own likings in the end, it one big jungle out there ^^
Good luck, hope it helped you some atleast