SEO and navigation with Cookies, session ID’s, JavaScript, Flash or Images
Some technical choices can make it difficult for search engines to completely index your websites pages.
See also the Google Webmaster Help Center.
Cookies and Search Engines
Search engines can’t store cookies.
If you use cookies in your user guidance (e.g. select language before entering the website), be sure to provide an alternative for the search engines.
Even if a user chooses a language and thanks to a cookie always opens the website with the homepage for this language, search engines don’t. Search engines always enter the website through the homepage (except if direct links to deeper pages exist on other websites).
As I’ll explain further XML site maps can help, but …
Session ID’s and Search Engines
The same observations for cookies are valid.
If you use session ID’s in your user guidance, provide an access to Google without session ID’s.
Often websites using session ID’s use long URL’s. This is bad practice for users (send link to a friend, save as favorite, …) and for search engines (duplicate content issues).
JavaScript User Agent identification and Search Engines
Directing the user to other pages (e.g. for layout optimization) based on JavaScript identification of the User Agent (Internet Explorer, Firefox, Opera, Safari, …) or Operation System (Windows, Linux, …) can be a technical sound solution. But Search Engines can’t execute JavaScript, so provide a default solution for the User Agent that does not execute JavaScript.
JavaScript links or JavaScript navigation and Search Engines
Search Engines don’t execute JavaScript, so they usually won’t follow JavaScript composed links. This is why you better not use JavaScript navigation on your website.
Provide natural HTML navigation, where JavaScript or CSS can be used as layout aids.
Flash navigation and Search Engines
Most Search Engines can’t read flash movies (see Google info). If you use flash on your website, make sure Search Engines can access all your pages.
You can provide an alternative version for Search Engines, but beware of the Duplicate Content trap.
XML Sitemaps and Search Engines
One might think all this can be overcome by using an XML sitemap.
But giving Search Engines access to all your pages through an XML sitemap as an alternative navigation method is a poor solution. Because if you provide the navigation on each page, this enforces the internal linking structure, and helps Google to identify your website structure and better distribute the page rank from your home page.
Website Navigation issues: Duplicate Content or Cloaking.
But if you provide an alternative for Google and the likes, be attentive to duplicate content or cloaking issues.
It could be a good idea to add a no-index tag (see observations by Matt Cutts) in the pages that are not intended for Search Engines (or specify exclusions in a robots.txt file). Even if Google cannot access the specific page from your home page, one of your fans might be linking to the page.
I still have to fine-tune my WordPress setup 
.
Images in Navigation and Search Engines
Many websites use fancy images in their main navigation. Usually a way to make sure that the page is presented correctly in all circumstances.
For example not all computers have the fonts a designer has in mind. By creating a button with the text the designer can make sure everybody will see the button as intended.
The bad news: Search Engines cannot read the contents of images. This can be mildly compensated by adding a descriptive ALT tag for each image, and maybe choosing a good file name for these images. But from an SEO point of view using images for your navigation is not the best choice.
A better choice for the design of the navigation would be natural HTML navigation and formatting with style sheets (CSS).