For my own use, I use pen and paper (for program design/brainstorming) and Inkscape if I need to have a diagram in a document (occasionally I use emacs' artist mode and ditaa for fun, too). At work, we use (org-wide) LucidCharts, which is decent enough at what it does (online diagramming tool with good collaboration abilities, can be embedded easily)
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[ 2.7 ms ] story [ 26.6 ms ] threadWill check LucidCharts for teams.
Gliffy - gliffy.com
Draw.io - draw.io
Creately - creately.com
RealtimeBoard - realtimeboard.com
LucidChart - lucidchart.com
Bubbl - bubbl.us
Textografo - textografo.com
Smartdraw - smartdraw.com
Edrawsoft - edrawsoft.com
Microsoft Visio
I've not used all of them. Looking for suggestions (preferably free tool).