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If you are using Adaptive Layouts and portal 6.5 or higher, you can modify them to alphabetize the communities. See this Knowledge Article:
How to use WebCenter Interaction Adaptive Tags to Alphabetically Sort a List of Communities (Doc ID 852287.1)
-Mike Headley, WCI Developer Support
You still have some hope...
You will need to do one of two things. First you need to get the UI source code. From here you can either extend the existing navigation scheme or create your own based on the scheme that you are using. It has been a while since I looked at the code, but I remember doing something similar to this, and it was not too difficult. I am sure others could post links to help you locate where there are some examples, etc. I just wanted to chime in and say that there are still some options.