Hello!
I've tried to run opencv 2.1 on my machine and found a bug(?) in
current cmake files and/or folder structure. I don't know how to
correct, but I do know what is going wrong and why
OpenCV can't work with system shared lib libjpeg<>6.2, because of
3rdparty/include/jpeglib.h. Though I have not selected BUILD_3RDPARTY
etc, it looks in that folder (possibly because of
ffopencv/CMakeLists.txt), then grabs jpeglib.h from there instead of
/usr/include or /usr/local/include.
And from here, we try to call system shared lib with old defines and
structs. Inside the libjpeg there are a version control, so
jpeg_create_compress/jpeg_create_decompress just quits, with an error.
But (surprise!) OpenCV doesn't handle jpeg errors as it really should.

So, my solution for now is just delete jpeglib.h from 3rdparty/include
and then make; make install. It works for now.