Sycamore - A systems biology computational analysis and modeling research environment, at Univ. of Heidelberg

Reactome - a curated knowledgebase of biological pathways
KEGG - Kyoto Encyclopedia of Genes and Genomes
PID - Pathway Interaction Database, at NCI
BioCyc - Large collection of pathway/genome databases
MetaCyc - Non-redundant, experimentally elucidated metabolic pathways

BIOBASE Suite - TransFac, TransPath, TransCompel, and ExPlain (NIH only)
KEGGanim - visualize and animate KEGG pathways, at Univ. of Tartu