CloneCD and
CloneDVD are two very different products.
CloneCD lets you make a complete backup and it works well. It creates as close to a
1:1 backup as is possible. It won't be 100% identical since you are removing protections and such but it is as close as it gets.
CloneDVD lets you transcode/compress to DVD-5. You can remove titles that you don't wish to have on your backup. You can remove unecessary audio streams, sub-titles, commentary, etc. In some cases removing the unnecessary audio streams and video titles allows you to fit an original DVD-9 onto a DVD-5 without any compression at all.
CloneDVD offers more power and versatility than
CloneCD but whenever you transcode you will lose quality. That's an inherent downside to compressing a backup to fit on a single layer blank disc.
Personally, even when I make a DVD-9 (DL) backup I still use
CloneDVD to rip and remove what I don't want and then burn it without compressing. I like a nice clean garbage-free backup.
So, the question posed was
"Which method is better?" That really depends on what you want in a backup.
It's very subjective. One thing is easy to say, however, and that is that both products are amazingly simple to use and much more complex than they appear.