How you procede depends largely on a few factors.
First, are you planning on Keeping the original CD's
but storing them where they aren't "out" and taking
up living space?
Because that by itself determins a lot of what follows...
IF you are NOT going to kepe them you need a far more elaborate
"defense in depth" backup system.
I Must say I STRONGLY RECOMMEND keeping them because as good as computer storage is it all fails eventually, no matter how carefully you back it up.
Second, what quality level do you need?
To be honest mp3 is very compact and takes a lot less HDD space, the highest standard bitrate is generally indestinguishable from the original source but takes up 22.5% as much space. (a compression rate of 4.5:1)
FLAC saves space 30-40%, but the TIME you'd take to make the FLAC files is better spend doing something else and simply getting Hard drives that much bigger and archive storing the files as wav, simply because wav can be converted to ANYTHING without any intermediate steps.
If you REALLY want Lossless I say get a Bigger HDD and store as WAV. (Yes, I'm repeating myself, giving my message that many more chances to sink in)
With HDD space being <$0.20/Gb it's hardly worth worrying
Yeah ripping to flac takes very little additional time,
but multiply that by 1000CD's....
I've made enough posts about breaking the process into an "assembly line" so that I won't labor over describing my methods.
you take 10 or 20 or 50 discs (how ever many you want to deal with
at one sitting) and you JUST rip them to an essentially empty HDD
You then as a seperate step create the compressed files of your chosen bitrate, then you do your tag editing (show me a ripping or compression program that does the tags perfectly... and I'll show you missing tag data)
THEN you move the music to the drive(s) you intend to play it back from... I say drive(s) "s" because only an idiot puts their created data in only one place, so you don't need a drive that'll hold all your music in your chosen codec and compression rate you need atleast TWO drives, one to use one to leave wrapped in a anti-static bag
wrapped in foam and stored in your bottom desk drawer.
The basic premise here is that HDD's fail.
and it's easier to back up your data than recreate it.
I'll admit to having my wav's on only one HDD, but I have all my original CD's and having them on the HDD is a convenience
(it saves me ~90second per album if I need create an mp3 file)
my mp3's are dupicated three times on active drives and several more times on "archive" HDDs as well as DVD+R backups
I avoid the inability to "tag" wavs by creating a directory structure to organize my files, an Artist/album/track heirarchy, so a file is identified in detail by it's location.
this division makes it FAST to find a particular track.
If I want AC/DC's "Hells Bells" I can find it PDQ.