After some more talk with Gerad, here is (I hope) final version of pyqwt3d 
installation for Karmic:
1. Get latest cvs version (some bugs were corrected):
cvs -z3 -d:pserver:anonym...@pyqwt.cvs.sourceforge.net:/cvsroot/pyqwt co -P 
pyqwt3d

2. Go to pyqwt3d directory and get and patch qwtplot3d:
make -f GNUmakefile qwtplot3d-0.2.7

3. Add
#include <stdio.h>
at the beginning of qwtplot3d-0.2.7/src/qwt3d_function.cpp

4. Go to configure directory and do the rest:
python configure.py -Q ../qwtplot3d-0.2.7 -lGLU -L /usr -I /usr 
--module-install-path=/usr/lib/pymodules/python2.6/PyQt4/Qwt3D
make
sudo make install

Now, someone who knows how just need to make a package...

-- 
Package python-qwt3d broken in Karmic
https://bugs.launchpad.net/bugs/478230
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