Should you primarily be backlinking and promoting your actual index/home page or specific individual pages within your website? I know in webmaster tools, it usually tells you your most highly ranked page, but I wonder does this highest ranked page determine where your home page will be ranked in the SERPS; or does it determine where all of your various other pages will be ranked as well?! Example: Would a specific page in your website with no backlinks pointing to it rank well in the SERPS based on a high PageRank on your index/home page?
A strong homepage will help your other pages getting ranked, but the effect is minimal unless you have a super strong homepage with very high pr and alexa ranking like wikipedia. While we are starting, if we depended on our homepage to rank our other pages, it could be very difficult and take a long time. The best bet would be to slowly build links for all the pages. But for best result, always place links to the direct pages of what people want.
I guess if you are churning out 1000s of pages then you should really opt to concentrate entirely on the home page in that case! It's amazing just how much control Google seem to have over webmasters, with the PageRank, SERPS etc.