J River and choosing encoder.

about to embark on a 1200++?? ripping session. expecting to spend a month on this so want to get it right the first time. not sure what encoder to use for ripping cd's. have tried APE and WAV so far and could not tell a difference sonically. however, the APE file is almost half the size?. from what little i understand regarding this topic, the lossless file types are suppose to sound/be the same somehow?. is there something i'm "not getting" here?.

uncompressed file size is not a real concern. would be happy to use extra space if there is some type of plus to it. storage is dirt cheap. am more concerned about the long term storage and functionality aspects of lossless vs uncompressed. also a bit confused about encoding in general. is one lossless type "better" then another?. is uncompressed FLAC "better" then WAV?. what's with all the choices?? or is that more then this computer illiterate old fart needs to know =)

current set-up and gear doesn't play into this for me. doubt i'll have the same equipment 5-10 years from now, but know i'll have the same music long after that. don't want equipment optimized files for today that could lead to a dead end down the road..

cheers
Lev.