Thanks for the tips. I'm also experimenting with custom post types and taxonomies right now. I'm very disappointed in how difficult they are to use. It's easy enough to enable custom types, but when you start to integrate them into a design and create permalinks, make custom queries, add paging, etc. it's overly complicated and difficult. I think WordPress has something great here, in theory only, because in practice these are still unrefined features.
Here's a quick example, if I make a custom taxonomy for a custom post type:
Post type: Products
Now I'll add a product called "Computers" and give it the manufacturers "Dell" and "HP". If I try and query all products for "Dell" and "HP" it won't. It requires a complex rewrite of the query to pull 2 or more custom taxonomy items in a single query.
Another issue related to this same problem, if I want to pull just 1 of those taxonomy items, lets say "Dell" then I would query "manufacturers" => "dell", but I won't get any output unless I specify "products" as the "post_type". That shouldn't matter. It should pull ALL post types using that taxonomy. This makes it impossible to have taxonomies that cross multiple post types and pull dynamically into a page without knowing which post types use that taxonomy and specify them as an array "post_type" => array("products", "services")