Proof

On Proof and Progress in Mathematics, William Thurston

Problems

Problems on Mapping Class Groups and Related Topics, Benson Farb, ed.

Questions in Geometric Group Theory, Mladen Bestvina

Problems in Geometric Group Theory Wiki

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

Blogs

Low Dimensional Topology

Geometry and the Imagination, Danny Calegari

Quomodocumque, Jordan Ellenberg

Software

SAGE example: Fibonacci numbers, Vince Lucarelli

SAGE example: Enumerating graphs, Vince Lucarelli

SnapPea, Jeffrey Weeks

SnapPy, Marc Culler, Nathan Dunfield, et. al.

KnotInfo

Knot Plot

XTrain, Peter Brinkmann

Trains and Dynn, Toby Hall

Danny Calegari's software

---The CompuTop.org Software Archive

Books

A List of Recommended Books in Topology, Allen Hatcher

Books for Graduate Students in Topology, Dan Margalit