Software

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

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

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

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

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

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

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

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

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