=====Removing products through the database=====
This should remove all the products and their related records.

<code mysql>TRUNCATE TABLE `catalog_product_entity`;</code>

Removing categories requires bit more actions. 

<code mysql>
TRUNCATE TABLE `catalog_category_entity`;
DELETE FROM `catalog_category_tree` WHERE `entity_id`<>1;
</code>

After that you will have to create root categories for your stores and assign them to stores in configuration:

admin menu / system / configuration / catalog - choose a store, choose Root Category.