(freeware solution)
you can use virtualdub with this filter:
http://shelob.mordor.net/dgraft/logo.htmlyou need to convert your pics to bmp (and put them in some sort of sequential order like image001.bmp....image00N.bmp) and vdub will take that as an input (also they will have to be of equal size), apply that logo filter with the bmp logo you prepared, then there is 'save image sequence' option which will get you the new sequence with the logo keyed in.
(btw, the 'transparent color' option is pretty useless so you will have to use the 'solid' logo for this kind of procedure, you can of course apply some general transparency (alpha blending))
hope that will help