If the URLs are friendly then you could try and rebuild everything but keep the important URLs static.
Failing that you can migrate the pages onto new URLs by using 301 redirects. Doing this shouldn't have too much of an adverse affect on your rankings (not in the long term anyway) and also means you can swap to nice looking URLs.
Alternatively if you want to swap over to a new domain then you can use 301 redirects and the change domain option in Google webmaster tools.
If you're changing the site architecture - say for example because you're editing the main navigation - you will want to make sure that you prioritize your important pages but that's really just SEO 101 and probably similar to what you have in place anyway.
Hope that helps but feel free to ask if you want clarity on something.