Regardless of what codec/bitrate you choose for you portable devices, you should absolutly rip to FLAC. Ripping a big CD collection is a giant PITA and you’ll never want to do it more than once. If you rip to a lossless format like FLAC you can always trancode to any lossy codec/bitrate you want for portable use. And you can change your mind as many times as you want without ever having to rerip. If you rip straight to a lossy format and then change your mind, you’re SOL. You can never get back quality that was lost and if you want to go to a lower bitrate, you’ve now applied two lossy conversions decreasing quality even more.
For accurate ripping, there are really only two choices: EAC and dbPoweramp. Use EAC with the REACT add-on if you are technically inclined and are interested in seriously customizing the ripping process with scripts (very powerful, but steep learning curve). Also, it’s free. Otherwise, dbPoweramp is much easier to use and is still fairly customizable, but it’s not free. Both are great and both will do an excellent job of ripping to FLAC, tagging, downloading album art, applying ReplayGain, etc.
For managing your media use something like MediaMonkey or Winamp. Both can handle transcoding from FLAC to MP3 (or anything else) on the fly while syncing your portable devices. Or you can batch convert your entire library at once and then manually drag/drop MP3s instead of syncing.
Also, keep in mind that it’s only going to be a few more years before 64 & 128GB flash players are common place. When that time comes, just stop transcoding and use your FLACs directly on your portable devices.