We (Raine & Wageman, the musical partnership I have) have finished recording 14 tracks for our third CD, and are just about to go through the process of sorting out the order we want them in.
Even though tracks are often played in shuffle mode, I still think there are enough people playing CDs from start to finish to warrant giving the sequence special attention.
The first track is one that we think represents our music best. The last track is one that has the best sense of climax or finality about it.
If there are similar-sounding tracks, I separate them, putting the better ones earlier on the CD. Generally I try to mix things up so that there is variety in dynamics and moods throughout, though sometimes it makes musical sense to have similar songs follow each other.