All things being equal, would there be any quality difference between compressing DVD-9 to DVD-5 using CloneDVD vs. other software such as Nero Recode 2? This assumes an apples to apples comparison of not removing any chapters or anything. Just a straight compress and copy of an entire commercial DVD to a single-layer DVD+R or DVD-R. Would there be any noticeable difference in quality of the final DVD?
Yes, depending on compression level (and the size of your television screen--and your eyes)
Both Shrink and Nero Recode produce better picture quality provided you're using deep or advanced analysis. The cost, of course, is the amount of time taken to transcode. Clonedvd2 transcodes faster. I recommend ripping with Clonedvd2 and then importing into Recode, if you're having problems with Recode alone.
Clonedvd2 also has an advantage if you're splitting across two discs and want to retain menus. Shrink and Recode can't do this.
For what it's worth, I can't stand compressing. If you truly care about picture quality, this method is much better (but more costly):