MockFlow Desktop and Web

Both online and offline (Adobe Air) tool for building wireframes.

Balsamiq Mockups for Desktop and Web

Axure for Windows

Omnigraffle for Mac

The Visio equivalent for the mac

HotGloo - The Online Wireframe App

Web-based HotGloo is a rich internet application designed to create functional, interactive wireframes and is intended for use in web projects to help visualize planning processes, co-work with team members, coordinate website contents with clients and provide a precise framework for designers and coders.

WireframeSketcher

Create wireframes & mockups with Eclipse.

Mockingbird

Mockingbird is an online tool that makes it easy for you to create, link together, preview, and share mockups of your website or application

ProtoShare - Web-based Wireframing & Prototyping

ProtoShare allows development teams to create simple gray-box wireframes and evolve them to rich prototypes during the website and web app development process. Interactive wireframes, clickable comps, and live website views are just the tip of what your team can accomplish to elicit superior requirements and reduce rework.

Lovely Charts

Although a chart program, lovely charts with its intuitive drag-and-drop interface makes wireframing an easy task.

Pencil

This is a Firefox add-on to do GUI prototyping and simple sketching

Lumzy

A flash-based wireframing tool.

Microsoft Visio

One of first tool available for wireframes.

Creately

Draw, share and collaborate on online diagrams. Easy web flow chart, network diagram, mockup, wireframe, UML diagrams like Class, Sequence, & data flow and process flow diagrams.

softandGUI - UXToolbox

Application design and prototyping solution. Quickly and effortlessly design, develop, prototype and document high-level User Interfaces of new and existing applications. Supports multiple Screen Resolutions and Devices. Export to PNG and Word.

ForeUI

Java based wireframing tool that works across Windows, Mac, and Linux.

LucidChart

Create diagrams and drawings such as a flowchart, mind map, network diagram, UML diagram, wireframe, user interface design and other drawings online with free flowchart software.

Adobe Illustrator

The real graphics gurus use Illustrator (and Photoshop). The power lies in the Vector art to make prototype design for as small as 320x480 to huge monitors.

PowerMockup

Plugin for creating low-fidelity wireframes in Microsoft PowerPoint.

Keynotopia

No need to learn a new tool: prototype cheaply and quickly for iPad, iPhone, Android, Windows Phone 7, Facebook and web using Apple Keynote, Microsoft PowerPoint or OpenOffice Impress.

InVision

InVision allows you to create stunningly realistic interactive wireframes and beautiful high-fidelity prototypes in a whole new way.