If you are comfortable using the Terminal application, incanting the following will get you a count of all the actions in the current database:
Code:
sqlite3 ~/Library/Caches/com.omnigroup.OmniFocus/OmniFocusDatabase2 'select count(*) from Task';
(press the "return" key after typing it all to cause the command to be executed, or better yet, copy and paste it from this message)
Do you have attachments for any of your actions? Some audio or photo attachments from your iPhone, or file or email attachments from the desktop can make the database size swell quickly. Unfortunately I don't know of a convenient way to figure out which actions are contributing the most to the file size.
As for the number of zip files in the MobileMe database, that will go up by 1 each time you add a new action, until all of the OmniFocus clients can agree that that action is "old news" so to speak (they've all got it synced into the "past history" part of the database, which is the .zip file that is much larger than the rest, typically). You have 3 OmniFocus clients, and there are apparently some optimizations yet to be made where the squashing down of the database doesn't happen as often as it should when you have more than just 2 clients. You can use the Coalesce database script posted elsewhere to do this manually, but if you aren't suffering from slow syncs on the iPhone, I wouldn't bother. My reading of the discussion is that the most important thing you can do to keep the sync speed acceptable is to make sure your clients get synced often, so that when you make changes on one client, those changes get synced to the other clients before you use one of the others to make additional changes.