Regardless of whether it is HTML, XHTML or HTML5 you find those annoying percentages littered throughout the place. Yet... I see an awful lot of websites dare not go near them. Yet I was always encouraged through uni to use them.
So which should I be using? Which would lead to better site design and why?
I'm aware to avoid the use of height although HTML5 really doesn't like me not specifying height if I want to use percentages.
Thanks for taking the time to read.
For fonts, you should use percentages (or em's, or rems) if you don't wish to fix the font size in Internet Explorer. If you use pixels, then users of Internet Explorer who change their default font size in their browser settings won't see the fonts increase/decrease. So this makes your text potentially less readable for users in that browser.
A great resource for this is the first chapter of Dan Cederholm's Bulletproof Web Design.
For layout, using percentages or em's will make your design more flexible to changing font sizes/localization etc. This is also covered in the book.
It really depends on what you do you want to build up.
Sometimes I need to build a website which could be read by people with certain disabilities. If for example also older people visit your site its good to use % so that they could zoom in your page and the layout still looks pretty.