Hey David,
Wish you were here is my second favorite (followed by Echoes, which really has some questionable stuff on it). Have a Cigar and Welcome to the Machine just seem out of place on that album to me. Everything fits just right on DSOTM. Without question the production is smoother on Wish You Were Here though.
An interesting side note, many people have made reference to the Wizard of Oz-DSOTM phenomenon, which I feel is an interesting set of coincidences, but nothing more. However, the final scene of Space Oddessy 2001, Jupiter and Beyond the Infinite, syncs perfectly with the song echoes. There is a high ping sound at the beginning of the song that should be timed to strike at the same time that the subtitle for the final scene of the movie. The combination of the two media is incredible, and they appear to be perfectly in sync. I do not think this is mere chance though, like the case of the DSOTM scenario. I recall reading in A Saucer Full of Secrets,the Pink Floyd biography, that Kubrick actually approached them to do the soundtrack, but they declined because they were trying to down play a science fiction band image they had acquired. Perhaps they later regretted it?
