Tools

Softwares for Space Physics Data Analysis

The SDDAS (Southwest Data Display and Analysis System)
IRF-U ISDAT (Interactive Science Data Analysis Tool)
QSAS: The QMW Science Analysis System for Cluster (Very powerful and flexible)
PAPCO (PAnel Plot COmposer)
FESTIVAL (A flexible and powerful software for solar data from SOHO and STEREO)
NAIF (NASA's Navigation and Ancillary Information Facility)

Servers for data analysis 

MIDL (Mission Independent Data Layer, Space Physics)
CACTUS (Solar, CME analysis)

Web servers or tools for spacecraft orbitography  

Solar system, planets, heliosphere:

3Dview multi-missions (Provides s/c geometry, planet maps, …)
SSS (Solar System Simulator)
SSC (STEREO Science Center)
IMCCE (Any solar system objects)

Earth-magnetosphere:

SSCWeb (Orbit viewer and data provider)
TIPSOD (SSC 4D Orbit Viewer)
OVT (Orbit Visualization Tool for CLUSTER,)
Conjonction Event Finder (GEOTAIL, CLUSTER, DOUBLESTAR, THEMIS)

Models, Simulation

CCMC (Community Coordinated Modeling Center)
CISM (Integrated data, models, and data and model explorers)
Tsyganenko model
Space Weather Models (Site from Italy)
Space Weather Modeling Framework, SWMF (University of Michigan)