In my opinion my method is Homepage
- Category A
---- Subject A.1
---- Subject A.2
---- Subject A.3
---- Subject A.4
- Category B
---- Subject B.1
---- Subject B.2
---- Subject B.3
- Category C
---- Subject C.1
---- Subject C.2
- Category D
---- Subject D.1
In that respect Google indexes the homepage, and the links A-D, on each link page contains another place google may go.
Whilst keeping the links A-D at the top of the page, google once finished A can see B, and C and so on.
Effectively within a week or so you're indexing all of your subject pages.
Worked for me.
Google mentions in their guidelines to build a sitemap page for your vistors, using this kind of structure would be very interesting from a sitemap view, where the user can actualy identify and understand the structure of your site, now google won't have a choice but to look at those pages :)
