Combinatorics of Polytopes  
Some (mostly on-line) resources
Books: 
-  B. Grünbaum,  Convex polytopes
(library link).
-  G. Ziegler,  Lectures on polytopes
(library link).
-  H.S.M. Coxeter,  Regular polytopes, New York: Pitman, 1948 ( library link). 
-  R.R. Thomas,  Lectures in Geometric Combinatorics, American Mathematical Soc., 2006 ( library link). 
-  Geometric combinatorics, edited by E. Miller, V. Reiner, B. Sturmfels. Providence, R.I.: American Mathematical Society; Oxford : Oxford University Press, 2007 ( library link). 
-  V.M.Buchstaber, T.E.Panov, Toric Topology (see Chapters 1-2).
Lecture notes and unpublished books: 
Some papers: 
Some special classes of polytopes: 
Associahedra, permutahedra, nestohedra, ...: 
-  C. Lange, Associahedral Structures in Algebra, Combinatorics and Geometry.
-  C. Lange, V. Pilaud,  Associahedra via Spines.
-  S. Fomin and N. Reading,  Root Systems and
Generalized Associahedra.
-  A. Postnikov,  Permutohedra, Associahedra, and beyond.
-  A. Postnikov, V. Reiner, L. Williams, Faces of Generalised Permutahedra.
-  V. Pilaud, Which Nestohedra are Removahedra?.
0/1 polytopes:
Fullerenes:
Coxeter polytopes:Open problems: 
Webpages: 
 Videos: 
-  Jos Leys, Étienne Ghys, Aurélien Alvarez,   Dimensions (9 short videos, including visualisations of 4-dimensional regular polytopes in videos videos  3 and 4).