What matters is that it is a loss-less format. I've used both lossless Windows MEdia Audio (.wma) and .wav lossless and they both do the job if your device supports either.
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I would use AIFF, as this supports tags and WAV (in itunes) doesn't. One downside of AIFF (and I believe WAV) is that the artwork stored in itunes isn't actually connected to the file, instead itunes maintains the information to connect them. So, it's possible to lose artwork for AIFF. But honestly, I've heard some degradation of sound with Apple Lossless and I just don't fully trust it anymore - and itunes doesn't support FLAC. There is an add-on that you can install that gets itunes to play FLAC files, and I may look into that, but haven't yet.
I've heard that best results can be had via ripping in Absolute Audio Copy (requires a PC platform) then bringing it into itunes and "fixing" the tags. If you're not going to do that, atleast rip with error correction on in itunes.
I also own a ipod touch, and have downloaded the app for it (called "remote") but not used it yet. Remote doesn't see what the format of the music is, it just operates itunes. So no worries there, use any format you want and it won't affect the operability of your remote.
What type of computer are you using? Good thing hard drives are getting cheap. Make sure to give yourself plenty of expansion room on your drive, and get a second for backup.
Good Luck, Peter
I have about 125 CD's loaded into my Seaport Free Agent Go Pro 500GB external hard drive connected (Firewire 800) to my MAC Book Pro computer and many more to go. It takes between 3 to 5+ minutes per CD using the AIFF format. I put the discs in and check back in 5 minutes. This is a very boring time consuming process. I recommend the AIFF format. I have a 2nd Seaport drive for backups.