On Proof and Progress in Mathematics, William Thurston
Problems on Mapping Class Groups and Related Topics, Benson Farb, ed.
Questions in Geometric Group Theory, Mladen Bestvina
Problems in Low-dimensional Topology, Rob Kirby
Problems In Groups, Geometry, and Three-Manifolds, Kelly Delp, Diane Hoffoss, and Jason Fox Manning
Problems In Foliations and Laminations of 3-Manifolds, Danny Calegari
Problems on Boundaries of Groups and Kleinian Groups, Misha Kapovich
Geometry and the Imagination, Danny Calegari
Quomodocumque, Jordan Ellenberg
SAGE example: Fibonacci numbers, Vince Lucarelli
SAGE example: Enumerating graphs, Vince Lucarelli
SnapPea, Jeffrey Weeks
SnapPy, Marc Culler, Nathan Dunfield, et. al.
XTrain, Peter Brinkmann
Trains and Dynn, Toby Hall
A List of Recommended Books in Topology, Allen Hatcher