Web design is sometimes called web architecture, equating websites as three-dimensional objects with different levels. The placement of these levels (web pages) and their navigation becomes similar to how one places rooms in a house, and goes through the house from one room to another. The other elements in those rooms - furniture, accessories, colors, etc. - also relate to how one arranges the rooms.
Christopher Alexander is an architect who has written an epic encyclopedic manual of how to design the optimal homes in his four volumes of The Nature of Order.
Here are the outlines of the Fifteen Fundamental Properties from Volume I of the Nature of Order. It is well worth to get the book and read the details, examples and photographs. I think they relate very well with web design.
1. Levels of scale: A balanced range of sizes is pleasing and beautiful
2. Strong centers: Good design offers areas of focus or weight
3. Boundaries: Outlines focus attention on the center
4. Alternating repetition: Repeating various elements creates a sense of order and harmony
5. Positive space: A background should reinforce rather than detract from the center
6. Good shape: Simple forms can create an intense, powerful center
7. Local symmetries: Organic small scale symmetry works better than precise overall symmetry
8. Deep interlock and ambiguity: Looping, connected elements promote unity and grace
9. Contrast: Unity is achieved with visible oppositions
10. Gradients: The proportional use of space and pattern creates harmony
11. Roughness: Texture and imperfection implies uniqueness and life
12. Echoes: Similarities should repeat throughout a design
13. The Void: Empty spaces offer calm and contrast
14. Simplicity and Inner Calm: Use only essentials; avoid extraneous elements
15. Not-separateness: Designs should be connected and complementary, not egocentric and isolated
