Most, because Debian is the only distro which strictly enforces their manpages and filesystem standards. And most source packages don't care much, resp. have other ideas
Lots. Because many upstream projects don't have their build system set up to work within a distribution (to get dependencies form the system and to install to standard places). All distros must patch things to get them to work.
Well, there are big differences in how aggressively things are patched. Arch Linux makes a point to strictly minimize patches and avoid them entirely whenever possible. That's a good thing, because otherwise, nonsense like the Xscreensaver situation ensues, where the original developers aggressively reject distro packages for mutilating their work and/or forcing old and buggy versions on unsuspecting users.
There seems to be a serious issue with Debian (and by extension, the tens of distros based on it) having no respect whatsoever for the developers of the software their OS is based on, which ends up hurting users the most. Not sure why they cannot just be respectful, but I am afraid they are shoveling Debian's grave, as people are abandoning stale and broken Debian-based distros in droves.
Needless to say, Zawinski was more than a little frustrated with how the Debian maintainers do things.
But honestly, this took 30 seconds to Google and was highly publicized at the time. This whole "I never heard of this, link??" approach to defend a lost argument when the point made is easily verifiable serves to do nothing but detract from discussion. Which, you know, is what this place is for.
I wasn't defending anything; searching for xscreensaver debian debacle yielded links that might or might not have been what you were referring to, They did not, however, yield a link to the JWZ site.
A fair few I expect, amongst actively developed apps/utils/libs. Away from sid (unstable) Debian packages are often a bit behind upstream but still supported, so security fixes are often back-ported if the upstream project isn't also maintaining older releases that happen to match the version(s) in testing/stable/oldstable.
How many Debian packages have patches applied to upstream?