tjena magnus, just a quick anecdotal experience to throw into the thread... for all its strengths and weaknesses, i'm pretty happy with svn-buildpackage, mergeWithUpstream, and a debian/patches dir. for a long time my biggest issue with this was having to maintain these patches across upstream changes, or introduce new patches. i (and i'm sure others) expressed this to the svn-buildpackage peeps, who responded with the svn-do command (dig around in /usr/share to find it), which i now use on a regular basis. svn-do + quilt has more or less removed the annoyances of debian-only + debian/patches in svn. sean  there's still the issue of clutter left behind in build-area, but nothing a cronjob can't fix up.
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