So, you've setup 4 columns, and a default page limit of 16 in your configuration somewhere but somewhere, you'd like to run a 3 column count with 12 products per page? Here's how you do it.
- Click your category in Magento Admin
- Switch to the Custom Design Tab
- Enter the folowing XML in the Custom Layout Update
<reference name="product_list">
<action method="setColumnCount"><columns>3</columns></action>
</reference> <reference name="product_list_toolbar">
<action method="addPagerLimit"><mode>grid</mode><limit>12</limit></action>
</reference>