I would like to migrate to Pardus without losing all my existing set up.
My hard disc is partioned as follows:-
PClos root 12GB/swap 3.9GB/Home 449Gb
So, using "advanced" if I set it up I to just format root and swap will I retain My home folder?
It should, but I would strongly advise making a backup just in case anything goes wrong. There might be issues with ownership and group, I don't know enough about PClos to know how it handles users & groups.
and will all my existing programs run correctly ?
That depends -- scripts should be just fine, c & fortran code will probably be OK, c++ might need to be recompiled & relinked depending on whether your previous distro had similar versions of the c++ libraries. (Of course if your previous distro was 64-bit then any compiled code will need recompiling).