Try Big Bad toy store. They still have most of the First and Second releases of characters and some side items. They will cost you more than matty but are way less than some of the prices you will find on evil-bay.
Also for some of the character you missed you got the right idea about catching the re-releases, they usually stay around at least a minimum of one hour depending on the figure and how fast their preivous release did.(I.E. He-man and Skeletor sell out real fast on re-release).