As you know, many search engines ignore JavaScript, and therefore won't follow the links at your site. If you use flash or images for site maps and links you will have the same problem. The use of NOSCRIPT can be applied, but used with care.
Sitemap Programs with Google
Here's what to do:
* Create a text site map that lists all the web pages. Place a plain text link to the site map on the index page.
* Search engines check the beginning of a page for sitemaps. A site map won't be found if it's at the end of a long page. Place the site map link at the top of the index page.
* Since you have more than the baseline 30+ pages, use Google's site maps tool. This allows you to submit a list of all URLs to the Google search engine.
* Create and account here https://www.google.com/webmasters/sitemaps/login and get started. Google's webmaster tools provide you with a free and easy way to make your site more Google friendly.
* Scan your site with this free tool and build your sitemap.xml file: http://www.auditmypc.com/free-sitemap-generator.asp. Place that file in the root of your site. (ex: mysite.com/sitemap.xml)
Thousands of Pages
Since you may have thousands of pages, and only see a few pages indexed, a site map program will definitely be worthwhile. Some companies spend a lot of money on PPC campaigns, realizing that SEO solutions can help them immensely. You should build a search engine friendly crawling environment by building a keyword rich site map. You would allow the major search engines to quickly find and index the pages, thus increasing the index counts at Google and other search engines.
Time to Ramp up
Initially, this will take a long time. You may see your conversions increase weekly, albeit slowly. Then, after a period of time, several months likely, you should see conversions increase to hundreds or thousands per week on a sizable web site. If your site is fairly new, Google places it in what they call the Google sandbox. It is done to make sure you do not spam and it is a valid site. For new web sites you won't rank high for many months - from two to five months. You will still gain from providing a clean site navigation with good content and backlinks. Tip: Make sure when you register a domain to apply with at least 5 years exclusivity. It shows you are serious (to the search engines).
Next Steps
Natural SEO and link building is still very valid - and building incoming links is always critical, especially when the engines have not yet indexed your page. You should go out soliciting high quality inbound links with the combination of deep interior links from niche sites and top-level links from directories. Additionally you may consider looking at URL and filenames page titles and metadata set ups. The site map configuration, the on page content and internal site linking. Google uses the site maps program and Yahoo has recently launched the site Explorer program at: http://siteexplorer.search.yahoo.com/
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