Solution:
Instead of using the standard link convetion: <a href="new-page.php">
Use the following format: <a href="<?=tep_href_link('new-page.php')?>">
If you really want to get creative and are looking at SEO specifically you can create custom pages for each product category by copying the index.php page and saving it as new-category-specific-index.php page. This page will function just like the default index.php page in osCommerce, to have the page return only the specific category you need, you'll need to use the following code:
<a href="<?=tep_href_link('new-category-specific-index.php','cPath=28')?>">
Remember to change the cPath=28 to the actual desired category or you'll get all the products.
