It sounds like you might be accumulating a large number of zip files in an uncompacted database. It's also possible that your database is just getting full of completed actions.
On your iPhone, on the Settings page for OmniFocus, in the Database section, what does it report for number of projects, actions, and zip files?
When you run the File->Archive command on your "main" Mac (right now, the Archive is not synced, so you should always use the same machine for the archive operation if you want to be able to easily get to all of your archived data in the same place), how many actions does it offer to archive for you?
If you go to the Sync pane in the Preferences window on the desktop and click the Show Clients button, how many clients are shown? Do any of them have a last synced date more than a day or two ago?
At some point, even with everything working as efficiently as possible, OmniFocus will be noticeably slower if your database gets large enough. One thing that some of us find helpful is to use the Terminal to turn on the LeaveEmptySelectionEmpty option, which eliminates the automatic selection of everything in the sidebar when you switch modes (and thus spares OF the effort of computing the display of most of the contents of your database). Instead, nothing appears in the outline panel until you select something in the sidebar. The time saved not redrawing all the data you didn't want to see more than pays for the time you might spend selecting a project or context in the sidebar. See Dennis' fine post
here for the details.