Modular Forms Software  
   HECKE can be used to compute basis of q-expansions and Hecke operators on fairly general spaces of modular forms.
   http://modular.fas.harvard.edu/Tables/software.html

TECC  
   Tiny Elliptic Curve Calculator, by Masanari Kida. Requires KASH 2.2.
   http://matha.e-one.uec.ac.jp/~kida/TECC.html

APECS  
   FTP site for Ian McConnell's MAPLE programs.
   ftp://ftp.math.mcgill.ca/pub/apecs

EIS  
   Software for computing Fourier coefficients of Eisenstein series attached to lattices by M. Kuss and J. Bruinier. Binaries for x86-Linux.
   http://www.mathi.uni-heidelberg.de/~bruinier/Readme.eis

Heegner Tools  
   Peter Green's Heegner Points package. Requires Linux and Pari/GP 2.1.1 or higher.
   http://www.math.mcgill.ca/darmon/programs/heegner/heegner.html

Ellipsa  
   Includes Primo, an implementation of ECPP, and CPG, class polynomial builder.
   http://www.ellipsa.net/

Periods of Hilbert Modular Forms  
   A package of PARI programs (v.2.1.1 or higher) for calculations described in "Periods of Hilbert modular forms and rational points on elliptic curves" by H. Darmon and A. Logan.
   http://www.math.mcgill.ca/darmon/programs/logan/logan.html

Code to Compute Heights on Elliptic Curves  
   Magma implementation of Silverman's algorithm to compute the canonical height on an elliptic curve over a number field or function field, by Martine Girard.
   http://www.institut.math.jussieu.fr/~girard/magma/anglais.html

Modular Quaternion Groups  
   Fundamental domains for Shimura curves, written in GAP. Documented with description of algorithms used and program structure, input and output. Results for quaternion algebras with discriminant up to 100.
   http://www.geocities.com/assafwool/Quat/Quat.html