It is resizing the image still... not with CSS. You can update that in: webassist/plugins/catalog/popularbox.php. I think you would be able to update line 37 to:
<img src="<?php echo('../../../'.$WAGLOBAL_Images_Folder. $row_MostPopularRS['ProductThumb']); ?>" class="popularImage" />
and webassist/plugins/catalog/featuredbox.php. I think you would update line 28 to:
<img src="<?php echo('../../../'.($WAGLOBAL_Images_Folder).$row_FeaturedRS['ProductThumb']); ?>" class="featuredImage" />
Then you could resize the images with CSS instead inline or by adding a style to the classes.
The shopping cart file is: webassist/plugins/shopping_cart/cart_editable.php. It is resized by the browser with a width specified in the html. You could remove that and resize it with css.