Since there hasn't been a better version of Gephex since 0.4.3 (though I haven't tried compiling the repository recently, last time was not successful), I've downloaded the source and hacked it until it built on Ubuntu 8.10 updated to today:
I haven't tested it all the way, especially the video input modules, but it probably works.
Most of the changes have to do with updates to gcc, where it treats classname::method in cpp files as errors, and some files needed to include stdlib.h or string.h that didn't before. Also some structure definition in libavcodec had to be messed with- the static declaration removed.
nasm, qt3 in the form libqt3-headers, and libxv-dev had to be installed (and other non-standard things for 8.10 that I already had installed for other purposes). For qt3, flags for the include, bin, and lib dir needed to be passed to configure.
I had to run configure in the ffmpeg library and disable mmx with the --disable-mmx flag, putting that flag in the top-level makefile didn't work. My configuration specific makefiles are in the tarball so you would definitely have to rerun configure to override them.
Next I'll be creating a new custom gephex module for my ARToolkit multimarker UI project.
I've tested this build more extensively, and have discovered that the Ubuntu visual effects that are on by default cause the gephex output window to flicker. To disable them go to System | Preferences | Appearance | Visual Effects and select none. It's possible I need to build gephex with OpenGL support and these options will co-exist better.
Also, my screencap frei0r module I've depended on extensively in the past updates extremely slowly on the laptop I'm using currently, it may be an ATI thing (I originally developed it on an Nvidia system).