Balsamiq Mockups is a simple, flexible, and collaborative software for building wireframes for websites, apps, and other digital media. Users may purchase a desktop license or pay a monthly subscription fee for the web app. Free desktop software is available for classroom use.
Creately is a web based diagramming tool with real-time collaboration to work together on diagrams. If you're not comfortable storing data on the cloud you can use the desktop version. It lets you create workflows, mind maps, concept maps, business process models, wire-frames, org charts and many more diagram types useful in research projects.
Jumpchart is a way to collaboratively design website wireframes and sitemaps, and includes the ability to create navigation menus, draft and organize content, and track changes. It could be used as a way to get a head start on building a website, even before a server and/or software are available. Jumpchart offers HTML exports, and a direct-to-WordPress export ($25+/month accounts only).