I use GoToMeeting daily, from home to work and work to home. My paid copy of PB4 is at home and now I have a 30-day trial running at the office.
The animations tend to degrade the user experience when PB is used remotely by generating extra communication traffic for non-essential graphic updates. Even locally, the animations slow down response time at least a little, especially in busier views (such as the Brownian [Brainian?] motion of numerous thoughts jockeying endlessly for position in the Expanded view).
In addition to the cheesy 3D movie blooming / bulging effect (which you can see is a great favorite of mine), there seems to be some other "business" going on around the active thought that becomes more visible when running remotely.
I haven't specifically checked PB with MS Remote Desktop Connection, but I'm assuming the same sort of response time degradation will (have to) occur there, too.
As this will be very easy to see in house I won't go overboard in this post.
Please add more options to control / disable animation effects both for aesthetic reasons (we don't all want dancing doodads all the time) and performance. Alternatively, provide a way to make the animation more "coarse" (i.e. update no more than once per second to five seconds rather than continuously).
P.S. Without wanting to be too presumptuous, I'm guessing that slow-motion test runs might also reveal some animation artifacts that could be corrected for a smoother experience both remotely and locally.