I found a number of free references on various subjects in mathematical physics, available free, legally, online.
Mathematics
Partial Differential Equations

Alexander Komech, and Andrew Komech,
"Book of Practical PDEs."
Eprint Lecture note 33/2007, 125 pages. 
Alexander Komech,
"Lectures on elliptic partial differential equations (Pseudodifferential operator approach)".
Eprint Lecture note 32/2007, 44 pages. 
Norbert Ortner, and Peter Wagner,
"DistributionValued Analytic Functions  Theory and Applications".
Eprint Lecture note 37/2008, 133 pages. 
A.D.R. Choudary, Saima Parveen, Constantin Varsan,
"Partial Differential Equations An Introduction".
Eprint arXiv:1004.2134v1 [math.AP], 204 pages. 
Robert Geroch,
"Partial Differential Equations of Physics".
Eprint arXiv:grqc/9602055v1, 57 pages.
Differential Geometry

Jürgen Jost,
"The principles and concepts of geometric analysis".
Eprint Lecture note 12/2001, 15 pages.
Note: "geometric analysis" studies things like Morse functions, etc.
Homological Algebra

Volker Runde,
"Abstract harmonic analysis, homological algebra, and operator spaces".
Eprint arXiv:math/0206041v6 [math.FA], 12 pages. 
Mohamed Barakat, Markus LangeHegermann,
"An Axiomatic Setup for Algorithmic Homological Algebra and an Alternative Approach to Localization".
Eprint arXiv:1003.1943v3 [math.AC], 30 pages. 
Joseph Krasil'shchik, Alexander Verbovetsky,
"Homological Methods in Equations of Mathematical Physics".
Eprint arXiv:math/9808130v2 [math.DG], 150 pages. 
R. P. Thomas,
"Derived categories for the working mathematician".
Eprint arXiv:math/0001045v2 [math.AG], 13 pages. 
Semen Podkorytov,
"On homology of map spaces".
Eprint arXiv:1102.1645v1 [math.AT], 9 pages.
KTheory

Max Karoubi,
"Ktheory. An elementary introduction".
Eprint arXiv:math/0602082v1 [math.KT], 22 pages 
Ioannis P. Zois,
"18 Lectures on KTheory".
Eprint arXiv:1008.1346v1 [math.KT], 137 pages.
Mathematical Physics
This is kind of physics stuff, kind of mathematics stuff, and doesn't really fit cleanly into either category.
Andreas Knauf,
"Number theory, dynamical systems and statistical mechanics".
Eprint: Lecture note 3/1998, 41 pages. 
Bruce Hunt,
"Geometry of super YangMills and supergravity".
Eprint: Lecture note 4/1999, 59 pages. 
Bruce Hunt,
"Conformal and gauge symmetry in D = 2 QFT".
Eprint: Lecture note 5/1999, 115 pages. 
Friedemann Brandt,
"Lectures on Supergravity".
Eprint: Lecture note 13/2002, 50 pages. 
Alexander Komech,
"Lectures on Quantum Mechanics (nonlinear PDEs point of view)".
Eprint: Lecture note 25/2005, 231 pages.
Physics

Christopher J. Fewster,
"Lectures on quantum field theory in curved spacetime".
Eprint Lecture note 39/2008, 62 pages.