Looking for resources/best practices with updating packages on my
  NetBSD 3.1 box.  I currently have downloaded the 6006-Q3 pkgsrc but may
  want to update some of the packages to those in -current (kde 3.5.4 to
  3.5.5 for instance).

Mixing 2006Q3 and head is asking for trouble.  Pick one or the other.
The issue is that the mk/ files and the buildlink3 files are related,
in that some package from current pkgsrc might depend on features in
current mk/.

But you certainly can update pkgsrc to -current and then only rebuild
some packages, as long as they are leaves.

  I understand there are several ways to upgrade, but nothing like
  'portupgrade' for FreeBSD (at least as far as I can see).  Just looking
  to some of the more seasoned NetBSD users for how they do it.

See pkgtools/pkg_rolling-replace.   It's only slightly like
portupgrade, but is intended to solve the same underlying problem.

-- 
    Greg Troxel <gdt@ir.bbn.com>