I'm interested in learning about topological QFT including Chern Simons theory, Jones polynomial, Donaldson theory and Floer homology - basically the kind of things Witten worked on in the 80s. I'm looking for pedagogical reviews rather than original articles. Though these things sit at the interface of mathematics and physics I'm interested in them more as a physics student. I remember someone asking for a suggested reading list for topological QFT in mathoverflow. The suggested papers were almost uniformly rigorous mathematics written by mathematicians. I am not looking for something like that.
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The relation is very deep and has a rich mathematical structure, so (unfortunately) most stuff will be written in a more formal, mathematical way. I can't say anything about Donaldson theory or Floer homology, but I'll mention some resources for Chern-Simons theory and its relation to the Jones Polynomial.
There is first of all the original article by Witten - Quantum field theory and the Jones polynomial. A related article is this one (paywall) by Elitzur, Moore, Schwimmer and Seiberg.
There are also some physical applications of Chern-Simons Theory. For instance, it appears as an effective (longe wavelength) theory of the fractional quantum Hall effect. Link invariants, such as the Jones polynomial, can be related to a generalized form of exchange statistics. See this review article: abs/0707.1889. See also this book by Lerda for more on this idea of generalized statistics.
Another interesting application is that Chern-Simons Theory in 3d is equivalent to General Relativity in 3 space-time dimensions. GR in 3 dimensions is quantisable and following a nice playground for quantum gravity.
http://ncatlab.org/nlab/show/Chern-Simons+gravity has a nice reading list about that topic at the References.
Maybe a good start is "Edward Witten, (2+1)-Dimensional Gravity as an Exactly Soluble System Nucl. Phys. B311 (1988) 46" but if you prefer more pedagogical material i think "Bastian Wemmenhove, Quantisation of 2+1 dimensional Gravity as a Chern-Simons theory thesis (2002)" and "Jorge Zanelli, Lecture notes on Chern-Simons (super-)gravities" are very readable.
Also pedagogical to me seems "Ivancevic,Ivancevic, Undergraduate Lecture Notes in Topological Quantum Field Theory" http://arxiv.org/abs/0810.0344 (already linked to at your link.)
Olaf has already given most of the references I would recommend. But in the case of Chern-Simons theories and knot theory, there are two (plus one) other very nice references. These are all written by physicist to physicists, so no modular functors, Cobordisms and so on.
1) Marcos Marino - Chern-Simons Theory and Topological Strings (arXiv:hep-th/0406005v4) Section II has a very good review of Chern-Simons theory and its relation to Knot invariants (and Rational CFT's).
2) Michio Kaku - String, Conformal Fields and M-Theory Don't be too scared by the title. Chapter 8 contain a very readable review of Chern-Simons theories and knot invariants. It introduces everything starting from a simple and intuitive starting point. For example shows how the abelian $U(1)$ Chern-Simons theory leads to the Gauss linking numbers by direct integration, and why one has to regularize with framing due to problem with self-linking. Chapter 12 is more generally about topological field theories, it discusses Cohomological Field theories, Floer theory, relations to Morse theory and so on. You might find this chapter a little more challenging than chapter 8.
3) Birmingham et al - Topological Field Theory This is a long, and a little old, review of many different topological field theories. It also contains a little bit about Chern-Simons theory but not as much as the other two above, as I remember.
I know many other good references, but they are more advanced. This is an advanced topic so most papers and books will naturally assume a certain background.
There's a third TQFT that Witten studied in the 80s that's worth spending time with: Gromov-Witten theory, which is concerned with topological variations on the nonlinear sigma model and string theory. The starting point is Witten, Topological Sigma Models. The most recent nice exposition I know of is Hori's et al's Mirror Symmetry.
Also worth a visit is Witten, Chern-Simons Gauge Theory as a String Theory, which shows the spacetime physics of a special case of these perturturbative string theories is described by a Chern-Simons theory. Marino's book is good here, too.
I personally find a book by Nash Differential topology and QFT very readable. It explains QFT very fluidly in my opinion.
From a physicists point of view, I would start with the following notes, which are Chapter 9 in John Preskill's Quantum Computing lecture notes: http://www.theory.caltech.edu/~preskill/ph219/topological.pdf, as well as the references within.
I would also mention Kitaev's paper https://arxiv.org/abs/cond-mat/0506438 as a specially influential reference. Appendix E of that paper is a good summary of the mathematical aspects of TQFT as used by physicists in practice. Quoting Kitaev,
Anyons may be described in the framework of topological quantum field theory (TQFT), which originates from Witten’s paper on quantum Chern-Simons fields  and the work of Moore and Seiberg on conformal field theory . Important mathematical studies in this area were done by Reshetikhin and Turaev  and Walker . For our purposes, it suffices to use a construction called unitary modular category (UMC), which constitutes the algebraic core of TQFT . This construction will be outlined in Appendix E.
Essentially, the practice in physics is to focus on the 'unitary modular category', also known as an 'anyon model', as a general language for talking about topological phases which can be described by TQFTs.
I found this paper in Numdam's (a mathematical journal compilation) archive, which encompasses all that you talked about and I found it clear, with some references to Witten as well. This paper goes much further in detail, but I did not read all of it. And this might help if you aren't bothered by learning by forum posts?