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