These colors are given by the default theme, but I can understand why you want to change them, and there is a way.
The PHPDoc scope is defined as "comment.block.documentation.phpdoc.php", while the 'regular' doc-block is defined as "comment.block.php". (see https://wiki.appcelerator.org/display/tis/Current+Theme+Scopes#CurrentThemeScopes-PHPScopes)
To setup your theme, go to the Themes preference page (under the 'Aptana Studio' preferences.
Click the '+' next to the 'Scope Selector' and a new element will be added to the list of scopes. Type in there 'PHPDoc', or anything you like. In the 'Scope Selector' text field, type comment.block.documentation.phpdoc.php. Select a color for your PHPDoc scope, and apply the dialog. The PHPDocs will now be colored as you defined.
(I'm marking is as 'invalid' since this improvement is already built into the Themes system)