Often when you do a site-wide update of your design, your content and/or your site structure, it can affect your website’s rankings in search engines negatively.
Try to keep your URL’s the same. Use 301 redirects for URL’s that have to change and ensure you redirect all changed URL’s to the content’s new location.
Don’t change too much too quickly. If you do a redesign, content update and rebrand all in one, too many changes are happening and you’re likely to lose rankings on many keywords.
Don’t change your domain’s WhoIs information. A changed WhoIs can give search engines the impression your website has changed owners, and they could reset all your rankings across the board.
Do a phased change-over: start with a small section of your site and evaluate, then proceed with the rest.
Keep your internal link structure in mind when doing a redesign. Internal link juice is important as it tells search engine spiders which pages on your site are important. Don’t divert attention from your key pages with a poor structure.
Track your web analytics and pay extra attention to 404 errors after the migration. This may indicate broken links, both internal and external, pointing to moved or deleted content.
Expect to see your rankings drop regardless of your preparations. A 25 to 30 day drop in search engine rankings is normal before levels return to normal or better.
Of course we can’t skip Google’s own recommendations:
Add and verify your site on Google’s Webmaster Tools.
Update your submitted Sitemap XML file to reflect the updated site.
Keep track of crawling errors to detect 301 redirect problems and 404 errors.
Create a custom 404 error page to try and minimize the impact of broken links.
If your site update is significant enough, publish a press release.
Use search engine marketing to supplement your (temporary) drop in rankings.
Update your robots.txt file to reflect any changes in off-limits content.
(Thanks to Barry Adams for these information)