Software/Webapp for creating computer science diagrams

OmniGraffle

• Gliffy should work for you. Many of the student's in my class used it and it worked out great.
• Microsoft Visio: Not web based, but quite powerful
• Dia: Open source diagramming tool

I made zwibbler.com for this. For a formal article, turn down the "sloppiness" setting.

For sequence diagrams try: http://websequencediagrams.com/