So is it that you have the fonts, but you still get a missing fonts message? Or does Indesign CS5 think you don't have them (so they don't appear in the font menus or in the "Find Fonts" dialog)? I use a font manager, and don't generally see this problem, but one client uses a different set of Arial fonts, and I always need to run through "Find Fonts" to do their work...
There are many different types(format) of font. e.g. truetype, opentype, postscript
The font used may have the same name, but different format.
The helvetica font on your G5 is a postscript version
while the helvetica font on your snowleopard machine is an opentype version.
Though it's the same name, indesign will tell you it's missing because technically it's not the same font.
If you don't use a font manager application, like linotype's fontexplorer, the only sensible place would be your default font folder. (font book)
If you'll be moving files between the machine often, i suggest merging your two font libraries together.
if you are migrating old files to the new computer, i really wouldn't bother. Just replace the fonts.
But do keep in mind some fonts have different baseline/kerning/tracking etc settings depending on the font format, so make sure nothing has moved.
I've tried a few free ones but they're largely useless and don't work properly.
I don't use a manager at home, but we have fontexplorer at work.