For OSX at least…
Step 1
Navigate to /Applications/Flex Builder 3/
Step2
Right click on the app, Flex Builder and select explore package contents. A new finder window should pop up with a folder called “Contents”
Step 3
Open the file Contents/MacOS/FlexBuilder.ini with a text editor of your choice.
Step 4
Add the following line :
-Duser.name=Seb Lee-Delisle
Except obviously you’ll probably want to use your own name 
Step 5
Save the file and restart Flex Builder. Now your automatically generated comments will contain your full name after @author!
Related posts:
Thanks for the tip! If you’re using the Flex Builder plugin for Eclipse:
1. Navigate to /Applications/eclipse (or wherever your Eclipse was installed
2. Right-click on Eclipse.app and select package contents
3. Open Contents/MacOS/eclipse.ini
4. Add the line:
-Duser.name=John Doe
Cheers.
Surprisingly enough, not everyone uses OSX
So for you windows users its:
C:Program FilesAdobeFlex Builder 3FlexBuilder.ini and/or C:eclipseeclipse.ini
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For anyone with FDT, it’s very simple and works on Mac or Windows:
Eclipse Preferences > FDT > Code Style > Code Templates (Misc)> Override System Username.
Just a quick note, if you decide to put your user.name entry in eclipse.ini make sure it follows after any -vargs statements you have i.e:
-vmargs
-Xms40m
-Xmx512m
-Duser.name=Paul Hayes
Otherwise it won’t work.
This also works for flash builder 4. Thanks seb!