My websites - full with unique content and constantly expanding, had a problem - plenty of pages gradually went to the supplemental index (ie. 50 out of 500 results were in the main index). After lots of experiments and reading below are my guidelines on how to organically do an onpage optimization or how easily to get more of your content indexed:
Paginated results
Ensure unique meta description wherever you can on your website, even on the paginated results: If you have article with lots of comments - on the 2nd onward comments page strip the article text leaving just the comments. This way you'll create a brand new unique content page, just like in forums.
Repetition and bold text
Put special attention to em(italic) and bold tags - they add weight to the web page and if repeated through the pages, they could trigger google's penalty filter. Remove repeated word occurrences such as: Reply to this comment, Vote, etc... - replace such text using unobtrusive JavaScript.
Unique heading and meta descriptions
Look especially at the headings like: H1, H2, and make sure that they are unique and not repeating.
Loading time
Improve loading time: inspect page loading time with Yahoo's YSLOW and Google PageSpeed browser addons and try to make most of the suggested improvements. Here is screen-shot from Firebug - http://www.getfirebug.com/ network monitoring feature (NET) to detecting slow loading elements:

how:
- make cache version of your pages
- use asynchronous Google analytics and social sharing buttons such as facebook, twitter etc.
- place all your JavaScripts at the bottom of your page - this way the page content will load first.
- gzip your css and js files
- beware of wordpress wp-cron.php file - it hogs the system CPU resources down and might get you banned from your hosting provider: just rename it or find where is used and disable all calls(includes) to this file, etc...).
Blogger users
If you use Blogger's hosting use this sitemap tool and submit the generated sitemap in Google's Webmaster tools. Benefits are that you'll submit your all posts which might be much more than the default 26.
Canonical urls
Check whether your website is listed in SERPS listings both via: http://yourwebsite.com , http://www.yourwebsite.com or http://yourwebsite.com/index.php
If that's the case you'll have to:
1. Manually rewrite all your: internal links to the already indexed/preferred (www or non-www) version.
2. Permanently redirect using .htaccess mod_rewrite your http://yourwebsite.com/index.html or http://yourwebsite.com/index.php page to the root domain of your indexed website URL (i.e http://www.yourwebsite.com/).
Link weight

Use Supplemental Results Detector http://www.seo4fun.com/php/pagerankbot.php to distribute evenly link weight between your pages.
Source Ordered Content
Display your content first to search engines via CSS - especially true for the new Panda update.
Example: http://layouts.ironmyers.com/100_percent_Layouts/layout/?id=5
Log your results
Write somewhere the date you've made those changes and check your statistics the next week to determine whether they are beneficial or not.
External tools
SEO site tools is a Google Chome plugin that has helped me a lot with the optimization of my websites. I'll show you how you can use it with a few basic steps:
1. Load the plugin into Google's browser: https://chrome.google.com/extensions/detail/diahigjngdnkdgajdbpjdeomopbpkjjc
2. Run your web page of interest.
3. Click on the right top corner icon. Then go to page elements. Here you'll find out more about your internal site structure. by Nevyan Neykov
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