Would it already be time for a long term solution that no doubt has been discussed sometimes in the past:
looking at configuration files in /etc and ~/.*, most of them are actually very simple. Instead of treating them as flat files with arbitrary content and *generating* the managed ones from debconf DB, you could pretty easily *manipulate* them in a more structured and fine grained way by parsing and unparsing them according to developer/maintainer specified metaconfiguration files. In addition to making merging of version specific changes easier, it also allows different configuration interfaces like Debconf now does but during package use, not just installation. In fact, I have previously experimented with such stuff on proprietary software at my work and our experiences there where quite encouraging: handling of blocks and order of configuration elements weren't as difficult as we though they would be, powerful metaconfiguration files could quite easily be created even with error-reducing GUI tools and while perfect solution apparently doesn't exist, comment preserving proved to be possible in practice. It seems there is already at least one current project for developing a tool like this: http://config4gnu.sourceforge.net/ Comments? - Jarno