Hi there !
In the past I found a script for blender 2.46 (but it didn’t play for blender 2.48) that could attach two meshes together (merging them) after selecting the non-manifold edges of the two meshes.
It was useful for example to attach two meshes like a head (with the non-manifold edges belonging to the neck) with the other non-manifold edges belonging to the body of the character.
Do you remember where I can find that script ? if I remember well it was in the official website, or if you know a script like that for blender 2.48 or also for an older version, no problem 
I know that there are other manners offered by blender inside the program like joining objects , union boolean tool , or auto merge option , but that script was great.
Thank you if you can help me
bye