Going to change the URL structure of your entire website, but scared about losing your search engine rankings? It's a common issue that I've seen impact both the largest and smallest corporations. Here are some common exchanges with site owners or web developers as how to approach it without losing the weight your old URL's have accrued over time.
Site Owner: We are changing all of the URL's on the site; will that affect our search rankings?
Changing URL's should always be a last resort. Search engines use the length of time a given page has been alive at a web address and the number of links from other websites that are pointed at that page to determine how important that page is. Although this weight can be transferred from an old URL to a new URL, it takes some work, and you will still most likely see a dip in your rankings for a short period even if doing it correctly.
Site Owner: How do I transfer the "weight" of our old pages to the new ones?
The only way to do it effectively is to leverage 301 Permanent Redirects. Most web servers have a means of implementing these. Anyone that requests one of your old pages will be automatically sent your new pages if they are configured correctly, including search engine spiders that will take the 301 as an instruction to transfer the accrued weight of the old URL.
Site Owner: I have 1,000 pages on my site, how many do we need to redirect?
This depends on your bandwidth. I always shoot for 100% coverage when possible, but in many cases that can be a lot of work for limited reward. If you can redirect the top 50% of your old URL's to the matching version on your new structure, and then redirect the remaining 50% to your new home page, that may be acceptable. This way the second 50% is all transferring its weight to your home page and not lost. Use your web analytics tool to determine the top landing pages.
Site Owner: How long will it be before my Google PageRank transfers over due to the redirects we implemented?
I wouldn't worry too much about this. The real test is whether or not your new URL's are showing up in Google's index. It can take some time for the PageRank servers to update, and PageRank is just one of many factors that go into deciding the success of your SEO landing pages. Nothing is better than just looking at the numbers. Has traffic from natural search fallen? How has the top entry pages from natural search changed? What are the top keywords pre and post move? Where do your pages rank in search results?