If your store contains a variety of items which have no real relationship to each other, then you have a couple of options available to you where categories are concerned.
Option one: The general site
If you want everything on one site, then you would simply create what categories you can and add an other items category for everything else.
When marketing such a site, you would focus primarily on ranking up your category showcase pages and related articles rather than ranking your site up as a whole.
There is nothing wrong with this approach, but it will likely take a bit longer to rank your entire site up with search engines than it would if you were a bit more focused.
Option Two: Targeted Sites
The main alternative to the general store site is to create multiple sites, one for each major category of products you carry. You would then create categories for those sites consisting of subcategories of the major category in question.
This typically involves a slightly larger investment ( multiple domains and multiple hosts ), but makes it a bit easier to rank each individual site up as a whole.
If you are just getting started and have little extra time or money, I would recommend the general site. However, if you have some extra time and money, you will typically get more for your money in the long run by creating multiple focused sites instead.