Anything to avoid 100 McBarf flags! Allowing every flag just once is the lesser evil. Only we will have to keep track of it and have to have a list of everything that is already there (preferably in alphabetical oder). And that list has to be updated constantly. I'm a sticker to detail and wouldn't mind doing it.
I like the idea of the game but I'd rather have that in addition to the "Flags..." not as the default feature. Two reasons:
1. How many of us will make it to a headquarter? (I am a manic waymarker, but even after three years I still haven't earned the "Corporate Headquarters" batch)
2. Puting a companies flag on the map is as far as I am willing to go for a free commercial. I bet you anything, after the obvious (McD, Carls Jr. and maybe three or four others) we will be swamped with 100 local real estate agents. At least where we live, Real Estate flags are a very common sight. I don't mind putting their flag on a popular website, but I wouldn't want to add their address to it without receiving provision :-)
I like the idea of everything that is not a political entity. Only now we'll have to go back to a remote area of Northern California because there is a hydro dam that proudly flies the flag of the California Department of Energy.
As far as Sport Teams go: Most professional teams have a flag of their team flying in front of their home stadium. It would give a second chance to everybody who missed logging a Professional Sports Venue in their home town.