Use the auto-generated interface to learn more about how to use the SOAP/XML-RPC interface. You'll need to know what your numerical UserID is. Right now you'll have to dig for it. That'll be changing soon, we'll probably just make you use your login or something.
See here: http://siteshuffle.com/api/invoke
For instance, if I wanted to retrieve suggested links in RSS format for my user "w12zard", I would use this URL: http://siteshuffle.com/w12zard/get/suggestions/rss.
Just like getting suggestions (see above). You can retrieve your SiteList via RSS or ATOM.
Add a link
This is how you add a link to a SiteList. If you decide to include the "http://" stuff in the link, be sure to URL encode them
Delete a link
This lets you delete a link from a shuffle. Unlike the ADD method, you'll need to supply a login
For example, if I wanted to delete www.example.com from my linklist I'd just hit this url: http://siteshuffle.com/w12zard/delete/linklist?link=www.example.com