My two cents, rip everything lossless. Full stop. Eventually, you will come to regret it if you do not do it right the first time. Whether that is AIFF, WAV or Apple Lossless really dosn't matter -- they are all bit perfect and cross-convertible. Storage is super cheap, get them ripped and archived, and know you have them. As beteen lossless formats, don't know any real sonic difference personally, but AIFF or WAV is thought by some to be better, as both are bit perfect and uncompressed. Apple Lossless is in fact lossless, but compressed to about (I thought) 1/2 the size. I use AIFF, but not sure it's important.
Now, all that said, when you put them on a portable unit (ipad/pod/phone, etc), I always set the synching preferences to automatically convert to AAC (the compression/trimming ratio from AIFF to AAC is about 10:1). This way, you have the benefits of everything archived lossless, while your portable versions -- where the format just ain't going to get you that much of a differnce and putting a premium on quantity over quality makes sense at least to me -- convert automatically. Just to re-tweak the math, let's guess that 500 CDs would run you roughly 300gigs AIFF (think I actually have > 700 just north of 350gigs, but anyway). If you set it to automatically convert to AAC when synching, you can easily fit all 500 CDs on a 32gig ipod. Just saying....
Finally, you could rip things twice and essentially have two archived libriaries on disk someplace -- but it's a lot easier to rip lossless and then have a program do the converting for you. As you can go lossless to more compressed, but not the other way -- just make sure to start with lossless and you only need to rip once. Wether you ultimately keep sets of each or just convert on synching is up to you. (The only practical difference that I am aware of is that synching takes significantly longer if you are also simultaneously down-converting to AAC. 300 gigs could run you over 10 hours, so a good overnight task.) Just my two cents.
