I would also recommend something like HTML::Template (or Template Toolkit) if you want to do some complex calculations/checking. But some of this can be done in SSI pretty simply. e.g.:

<A HREF='http://affiliateprogram.com?id=<!--#if expr="$QUERY_STRING" -
+-><!--#echo var="QUERY_STRING" --><!--#else -->50<!--#endif -->">Link
+</A>
[download]

You can also use SSI to check to make sure that the query string matches a specific regular expression, etc. See http://httpd.apache.org/docs/mod/mod_include.html for more info.