Books:

D. Sornette
Critical Phenomena in Natural Sciences: Chaos, Fractals, Self-organization and Disorder: Concepts and Tools
Springer-Verlag, 2nd Edition, 2003.

The full text is also available on Google books here.

Articles:


General themes:

P. W. Anderson (1972).
More is different
Science, Vol. 177, pp. 393-396.

M. A. Bedau (1997).
Weak Emergence
In James Tomberlin, ed., Philosophical Perspectives: Mind, Causation, and World, vol. 11, pp. 375-399. Oxford: Blackwell Publishers.

I. Couzin (2007).
Collective Minds
Nature, Vol 445, p. 715.

J. M. Epstein (2008).
Why Model?
Santa Fe Institute Working Paper.

Scaling:

M. Mitzenmacher (2003).
A brief history of generative models for power law and lognormal distributions
Internet Mathematics, Vol 1, pp. 226-251.

M. E. J. Newman (2006).
Power laws, Pareto distributions and Zipf's law
arXiv preprint.

A. Clauset, C. R. Shalizi, and M. E. J. Newman (2007).
Power-law distributions in empirical data
arXiv preprint

Online writings and gatherings of writings:

The Complexity Digest rounds up articles from across the spectrum of complex systems.

Peruse Cosma Shalizi's notebooks for a sober view of complex systems and all things related. See in particular:
Complexity
Complexity Measures