I want to be able to compile ffmpeg and mlt to different locations then the ones that are installed by the package manager. I did this with
export LD_LIBRARY_PATH=/usr/local:$LD_LIBRARY_PATH
./configure --prefix=/usr/local
make
sudo make install
But kdenlive needs to be compiled with cmake, and I cannot find out how to force cmake to look for those libraries in the new locations.

Ok, I found my own answer from this post: http://kdenlive.org/forum/parallel-installation-sources-and-packet-manag...
The reason I wanted to do this was because the build-kdenlive.sh script failed while trying to configure swfdec. It said that it could not find the package glib-2.0, even though it was installed on my machine (the developer packages as well).
It turned out that a similar answer applied here as well: In my Opensuse 11.4 (64 bit) PKG_CONFIG_PATH needed to be set to /usr/lib64/pkgconfig for the build-kdenlive.sh to work:
export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:$PKG_CONFIG_PATH
If you want to install just kdenlive from source with different library locations, PKG_CONFIG_PATH needs to be enlarged to include the non-standard locations of the other libraries before doing the cmake step.