I style my taxonomy terms as boxes, so I don't need comma between them.
Could somebody give me any advice?
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Here's a nice blog post on styling taxonomy in node.tpl.php (or node-contenttype.tpl.php): http://oliverdavies.co.uk/blog/how-style-drupal-6s-taxonomy-lists-php-css-and-jquery
Looks like you should check your node.tpl.php for something like
<?php if ($terms): ?> and then you might see where the commas are being added and strip them out. This will depend on what theme you are using.