I use MapTool for all my games but C&C and have been using it for a little over 4 years. I won't be starting a new game until after the new year and it will be Savage Worlds Hellfrost, not Pathfinder. If you would like to play, let me know and I will keep you in mind when I announce it.
I use it every week for a F2F game. We use a projector setup replacing traditional miniatures. My players REALLY like the LOS and Lighting it adds. I now have people seriously thinking about races with darkvision and the feat deep sight as vision is so important and realistic now.
And if you are still on Build 63, you REALLY need to move on up to b87. There are SO many new options.
There's a couple of Frameworks for Pathfinder, 1 complicated and a couple simple bare bones. And one that works with Hero Labs.
And you will want to check out Wolf42's Bag of Tricks. It adds a lot of nice options to manage your campaign.
I just released a custom beta JAR as well that now allows us to edit VBL (Vision Blocking) on the fly via Macro's. A key example is you click on a door, it swings open (the image rotates) and the VBL is erased showing you the room. Another click closes the door and applies the VBL again.
I think we're going to see a lot of cool stuff in the coming weeks from the macro coders with this...
Here's a sample of it in use: https://docs.google.com/file/d/0B2c01YG2XtiJd2dqeUFqaUtLVXc/edit
We use MapTool/Skype every week to bring in our one player who moved to Baltimore. It does take a bit of getting used to, and I don't bother with lots of macros (I still can't figure out the code).
My big beef with MapTool is the general lack of documentation (which is often a problem with open-source solutions).
I used it (along with Skype) once for a two-part session of a normally face-to-face game I'm running. The two parts happened to be separated by 9 months and one person moving away, but we were able to pick right back up and finish that session. On the other hand, each time we had a bunch of issues with getting it connected, getting people set up with their tokens, tracking things, etc. Nothing that familiarity wouldn't have fixed, but it's very hard for everyone in the group (GM included) to be learning it at once. I had one player who had used it before, so he had some idea of what it could do, but no idea of how to set all that up.
Overall, I'm just going to use roll20 if it comes up again. Much simpler, much easier to get people to use. On the other hand, if I were to start a new campaign that was intended on being entirely online, I might consider sticking with Maptool, because there would be the time to develop that proficiency, and it does have more features (for the time being).