Having just read that installing Mavericks has resolved the mouse issue for one reader, I decided to reply.
I have had intermittent disappearances of my mouse cursor as well on my iMac from when it ran Lion to Mt. Lion for years.
Upgrading to Mt. Lion didn't fix the problem, but did cause a lot of issues with my Adobe applications at the time, forcing me to upgrade them from CS5 to CS6 due to numerous incompatibility issues.
Upgrading to Mavericks is not an option I want to try despite the thousands of one and two word reviews on the App Store such as 'Great!', or "Best OSX Ever!", for two reasons:
1: A recent attempt to just synch my iPad running IOS6, either with the 'Cloud' or with my iMac failed. Despite contacting Apple Support, and several hours of work, the results were a forced upgrade to IOS7 on the iPad and a total loss of it's data, despite backups still residing on my iMac, and a backup that was on the 'Cloud' just before the forced OS update. The techs told me they have no record of a backup to the 'Cloud'. Not good.
2: After seeing the IOS7 features, I don't like the cosmetic changes, nor will I have a use for many of the 'improvements'.
But I digress.
The mouse cursor still, and always has disappeared since I've owned my iMac.
I too have tried everything.
It has happened frequently when using Adobe applications, which I update constantly.
I have recently had to set my display size to 'the best for the built in display', instead of scaling it to a lower resolution, to accommodate major unresolved issues with several 'Blizzard' games I play. This has made everything from the cursor to the system text very small and hard to see.
Using System Preferences ->Display -> Cursor Size, I enlarged my cursor. Unfortunately there is no way to enlarge system text without messing with things you shouldn't have to.
The mouse now disappears constantly when moving over pages in Safari and between any app.
You can see that it is functional, as hot spots will change when hovered over.
The only way to get the cursor back is for me to move the cursor to where I believe the desktop is, then click, and it re-appears. If I hover it over the current home page at Apple.com, it will disappear after it has activated a hot spot, and reappear as the default 'hand' when moved over an image hot spot.
When I reset the size to the smallest, at least Safari works again, until I start switching between apps.
Life goes on and we now have colored iPhones available that will be obsolete and in land fills within two years. Woohoo!