Like Robert mentioned, if you can group them and republish your services, that would be the best bet.
However, if you cannot for whatever reason, you could create multiple layer lists using the default layer list widget that would allow you to group the individual services together as necessary. For example, you would have (1) layer list for geographic data, another for demographic data, etc. You could have them side by side in your main widget container or stack them in a new widget group. I've done both to clean things up a bit.
Its not the ideal way to go about it, but if you are forced to use an excessive amount of layers then it will allow you to control them to some point.
I don't remember how to post code in a nice manner so I'll just copy and post an example:
<widgetcontainer layout="float">
<widgetgroup label="Misc Tools" icon="assets/images/i_options.png">
<widget label="Draw & Measure" url="widgets/eDraw/eDrawWidget.swf" config="widgets/eDraw/eDrawWidget.xml" icon="assets/images/i_measure.png" top="150" right="20" />
<widget label="Bookmarks" url="widgets/Bookmark/BookmarkWidget.swf" config="widgets/Bookmark/BookmarkWidget.xml" icon="assets/images/i_bookmark.png" top="200" right="20" />
<widget label="Print" url="widgets/Print/PrintWidget.swf" config="widgets/Print/PrintWidget.xml" icon="assets/images/i_print.png" top="250" right="20" />
</widgetgroup>\
If you are using something like XML Notepad it would look like this:
An ESRI example with widgetgroup
Granted I don't use the App Builder when working with the Viewer for Flex, its too limiting. I edit the tag references via XML Notepad.