For the most part I just use text links targeted at catagory/niche/specific products. Also about 15 co-branded stores. I'm just starting to get into the FHGs right now so we'll see.
EDIT: Just woke up, forgot a few things
I'm also using the Store Search plugin.
I like being able to customize the stores to match your site colors logo and all.
http://www.mallcom.com/samplestores.html