PathVar
Microarray analysis of pathway expression variance

http://pathvar.embl.de/

EnrichNet
Network-based enrichment analysis

http://www.enrichnet.org

ArrayMining - Online Microarray Data Mining
Ensemble and Consensus Analysis Methods for Gene Expression Data

http://www.arraymining.net

PathExpand
Extending cellular pathways in interaction networks

http://www.pathexpand.org/

TopoGSA
Network topological gene set analysis

http://www.topogsa.org/

bioCompendium 
The high-throughput experimental data analysis platform

http://biocompendium.embl.de

Arena3D
Visualizing biological networks in 3D

http://arena3d.org

Martini
Biological Knowledge from Gene Sets

http://martini.embl.de/

Caipirini
Using gene sets to rank literature

http://caipirini.org

HIV mutation browser 

http://hivmut.org

Human-gpDB 
A database of human GPCRs, G-proteins, Effectors and their interactions

http://schneider.embl.de 

Reflect
Highlights protein and small molecule names

http://reflect.ws