Colours
What's your favourite colour? Whats your second favourite colour? What is the colour of pages of a book? What is the colour of writing in a book? Why are books mostly almost-white pages and black ink? Ok, so mostly with books its a cost factor. Coloured inks and printing costs more. So its not quite the same as the Net, where it costs the same amount to use red as it does white. But quite a significant factor is the readability issue.
You might want to look at some colour wheels to get the idea about colour which go together, blending together - shades of one colour, being either next to each other, or contrast and go together and are on opposite sides of the colour wheel.

Fonts
Don't use mad whacky fonts unless you're actually using them in button graphics. They won't show up unless they're installed on the users computer. This font will show up as either arial, helvetica or sans-serif.

Graphics
Gently does it on the graphics issue. Don't put huge pictures on your web site unless you've warned people about it. Use thumbnails to display pictures, allowing users the option of viewing a big picture. Learn the transparent gif trick to make tables work for you.

So how to decide on a colour scheme and layout
Obviously the html has to be within your limits - but that doesn't mean you shouldn't be brave and try new things. Colours and layouts are entirely up to you. Look at web sites you visit in terms of style, layout, navigation. Look at what you like, and have a guess as to what the code is. You can always view the source of html pages online, or save them and look at interesting pages. If you decide you like a colour scheme, make sure it works for your site. Pastel shades might not look right on a rugby site, but might look ok on a wedding site. When you've decided on a scheme, try it out. Make a mock up page. Have a look at the colours and your site title. Does it please you? Ask someone else for their opinion. Think about how it would look printed. Then put away and try something different. Compare and contrast. Which works best? Which do you find most pleasing? Happy with it? If not carry on thinking.