According to the site, you can use the Web Builder to:
Browse catalogue of every module in Dojo, Dijit and DojoX, using text searching to quickly filter the entire results. Simply select desired modules to include those in a custom build. Currently serving over eight hundred modules for the 1.6 release.
Automatically generate custom Dojo builds using our remote service, no need to open terminals and run the intensive build system locally. When the build is complete, it will automatically start the download of the result. Progress indicator keeps you informed of status during a custom build.
Auto-analyse existing Dojo applications to discover module dependencies. Provide the Web Builder with a remote URL, upload a HTML page, zip archive or an existing build profile to have the tool show you any Dojo Toolkit or custom module dependencies uncovered. Custom builds using the results will automatically include your custom modules.
Customise builds even further in "Advanced Mode". Want to include a Dijit theme with compressed CSS? Want to use Google's Closure compiler for aggressive compression? Want to build multiple application layers? Want to generate builds for the WebKit platform? Need to generate a cross-domain build? Switch to using the Web Builder in "Advanced Mode" to unleash the ability to heavily customise build parameters.
Here's a video explaining it a bit more:
Web Builder - Custom Builds from Toolkit on o.