MacPyMOL is mostly based on PyMOL open-source code, but there are a few Mac-specific proprietary pieces. 
So to the extent that your suggestions also apply to the Open-Source version, please consider using the PyMOL Open-Source Trackers linked from the main web site:
Click on "Features" (Tyrosine) and then "Add new" (or Add Artifact in the new version) and complete the form.  Having a SourceForge account will enable you to receive follow up messages, but you can make suggestions anonymously without having an account.
For suggestions which pertain to the proprietary aspects of MacPyMOL (e.g. direct QuickTime export, Cocoa-GUI, Mac-only funkyness, etc.), please email those ideas directly to support@delsci.com

From: Dan Kelleher [mailto:Daniel.Kelleher@umassmed.edu]
Sent: Thu 2/26/2009 11:54 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Where is the preferred place to E-Mail suggestions to Improve the MacPyMol Software ?

I've Forgotten,
Where is the preferred place to E-Mail suggestions to Improve the 
MacPyMol Software ?

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