I recently did some digging for available flowchart programs here on the site. This generally defined as having the ability to build from a traditional item set (box, circle, diamond, etc. as above) to build connections that move with objects. This isn't intended to cover Visio replacements, just handle one thing that Visio does well.
- Pencil - simple and easy to get started
- LibreOffice ("Draw" component) - lots of flexibility, but a bit of a learning curve. Does a lot.
- Softmaker FreeOffice - Presentations tool
- DynamicDraw Portable - clearly built for flowcharts but has a learning curve
- Edraw Mindmap - has some excellent tools, really impressive
- yED
- Diagram Designer
- DevFlowcharter
- XMInd - has a decision tree and a cause-and effect analysis
- ONLYOFFICE - (not portable) has some shapes and will line up items in the presentation tool
- Gliffy - web-based (Commercial)
EDIT: Missed yED, Gliffy, and Diagram Designer.