Clear flow charts can go a long way in explaining the randomization arms of your study or any other group allocation. There are 2 free options:
RFFlow is a free program "for drawing flowcharts, organization charts, and many other kinds of diagrams." You can download a free demo version which does not expire but has a slight limitation on the number of figures in each chart (not a significant hurdle unless you plan to make very large diagrams).
Gliffy is a web-based tool for flow chart design. Similar to the web word processor Writely, you can invite colleagues to collaborate on a diagram. "Gliffy also stores multiple revisions of the same chart making tracking changes easier. You can even link your flowcharts from your blog or wiki", writes the Digital Inspiration blog.
I used Gliffy to illustrate a post about DPP-4 Inhibitors for Treatment of Diabetes. The diagram is now on Wikipedia.
Draw Anywhere is another web site for making flowchart diagrams in the browser.
Gliffy: Web-based Microsoft Visio - Google interested? Digital Inspiration blog.
Quick and simple online drawing. LifeHacker.com
Bubbl.us - Easy 2 Make Flow Diagram. Go2web2.
Create Animated Charts and Flash Graphs for your Website. Digital Inspiration, 2007.
Make Flowchart Diagrams in the Browser with Draw Anywhere. Digital Inspiration, 2007.
How to Use Bubble.us to Make 2008 Your Most Productive Year Ever. LifeHack.org, 01/2008.