I decided to try CGI::Session out and was wondering if the user does not have cookies enabled, then that means I would need to pass the session id through the query string?

Only if you want to brand a user the way a cookie would. I find it easier to force the user to enable cookies.

I'm assuming HTML::Template would be best for this? Are there any other options that may be better/ more efficient?

For what, templating? Try searching for best templating system (or even super search) and similar keywords, it should bring up plenty of relevant previous discussions.

update: Here are some promising results

• Survey of Surveys on HTML Templating systems
• Best templating system?
• Templating system opinions on mod_perl mailing list
• Choosing a Templating System
• Templating Systems
• Templating system for generating C code?