Colour:
Light colours. The coulours must be from a similar colour-group (like all shades of green, for example) with maybe 1-2 darker, complementary colours for a contrast and highlighting. I despise dark sites, especially background #000000, text #FFFFFF. This includes varieties like cyan or yellow text and a black background. Goes for forums too, of course.
Light colours give a sense of an expansive, fresh, clean site. It puts the visitor in a better mood too. Be careful with what colours you choose.
Positioning:
3-columned layouts are pretty bad and overused in my opinion. Actually, Serebii.net's one is the only one I've seen and liked so far. This might be because of the site's font, which greatly appeals to me, though.
There are many layout possibilities. A layout I really like is
http://www.zymic.com (not the layouts they provide, the actual page layout) probably because the images they used to give table cells a distinct feel. A layout as pleasant as this one is a pretty rare thing to see these days.
My favourite layout-type is several tables, one below the other, with rounded corners. Simple and very attractive if you make it right.
If you ask me, I'd choose standard <table>s over any fancy CSS layout any day. CSS is becoming overused. CSS can be (and probably is) your best friend when planning stuff like how your text will appear, how much of a border your images have, how much padding to put between two blocks of text, etc. But moving a lot of recognising features of a web page (tables, for instance) into their CSS equivalents/near equivalents annoys me. Cascading Style Sheets should serve as an extension of your HTML document to do things which HTML does not allow you to.
Another thing I'll mention (to webmasters-begginers, reading this) that isn't directly what this thread is about: JavaScripts. Use... Them... Sparingly... If you want your page to "seem alive" to your visitors, and you wish to write a script to, say, change and apply options which are members of a <select> tag, fine. But if you have recently been to dynamicdrive.com and want to put snowflakes, bubbles, dancing cursors, embedded music, random earthquakes, alert boxes, etc. on your site... PLEASE DON'T. This goes for disabling right click too. It makes your site messy, to say the least. Unfortunately, JavaScript is quite strongly associated with adverts, spam, confusion, random images, links moving around, anchors not pointing where you as the visitor swear they pointed last time (example of Math.random used where it shouldn't

), etc. - this is because JavaScript is (unfortunately) being used for those purposes. With every <script> tag less that you have, your visitors will have one less headache. [/rant]
Navbars
Having a unique navigation bar of a page is important to me. I hate boring navbars, so I endeavour not to make that mistake with my own. Using something like Flash to make a navbar is a good idea (only if you're good). I saw a navbar once that had been made in MSPaint under 1x zoom with a pencil tool. Unique, but horrible.
When it comes to the navbar's position, I prefer to have a navbar vertically along the top of the page (just one that is not just text spearated by bitwise OR operators [I'm referring to "|" signs]).
To sum it all up, I believe colour and images are the most important things on any site (excluding content). Only in a few cases can the content itself justify the non-existance of a proper page design.