Most of what makes these sites seem so nice is that they're familiar and "modern web 2.0". Scribd is very Diggish for example.
Inkscape is like magic for creating nice logos, if you keep it simple. Truly anyone can do it. Use a color scheme tool like http://kuler.adobe.com/. Don't invent a totally unique design, imitate someone at first.
Anyone who can code well can easily reproduce nice simple site designs. Overcoming the "I can't design" mental block is the hardest part. Becoming a real design master takes a lot more effort obviously.