So far I have worked on three games to completion. I am about to enter my third year of university for games programming, after which I can take a year out to do an industry placement (assuming I can find one etc etc).

So right now I want to build up a portfolio site to show potential employers what I'm capable of and show case the games I have made/making. So my questions are thus:

Does it matter if a website is made in Flash or coded in HTML/CSS?

Does anyone know any good templates that can really show off your work?

These are utter newb questions I know, but ones I felt the need to ask regardless.

If you're not developing Flash games specifically, I'd say it's better if you don't use Flash for your portfolio. IMO, Flash websites are intrusive, ineffective and bloated. A clear and simple HTML/CSS web site is much better in my opinion. There are a lot of CSS template sites on the web, for example (after a Google search) www.freecsstemplates.org or free-css-templates.com. All free CSS templates on these two sites are published under the Creative Commons Attribution license.