Generally SEO's tend to look at the 3 major search engines - Google, Yahoo, MSN/Live (or what ever name its called today)
Search engines these days tend not to like auto submission software and prefer to detact your site naturally via links from other websites.
So the best way to get your site indexed is to get links into your website from others (it also will help your rankings too)
You can also create a Sitemap to help them find all of your pages and submit it using the top 3 search engines webmaster tools: (click links for each)
Google Sitemaps - Requires a Google account (Gmail or what ever)
Yahoo! Site Explorer
- Requires a Yahoo account (you@yahoo.com)
Live Search Webmaster Center
- Requires an MSN/Live account (Hotmail or what ever)
Each of these websites provide other tools you can use to help your website - search as pages indexed, links in, crawl errors and others.
Also on most search engines you can search for the following:
To find out if your website is already listed - as if you are submitting your website while already listed, the search engines wont like that very much.