Google's usage guidelines state:
Web sites and applications using each of the Maps API may at no cost generate up to 25,000 map loads per day for each API
So if I have two sites on a single web server, do they share the limit of 25,000 map loads, or does each site have its own limit of 25,000 map loads?
Did you read the part when the query limit is exceeded? The Api simply doesn't compute a query and Google isn't sending a bill to you. You have to apply to the paid program yourself. I want to say you can show your user a brief explanation when that happens or redirect them to another site. Anyway it's written web sites not server so my opionion is you don't have to worry about this.
The limit is per API key not per website. But you have to "exceeded the limits for more than 90 consecutive days". Also "Non-profits and applications deemed in the public interest are not subject to these usage limits".
See the FAQ: http://code.google.com/apis/maps/faq.html#usagelimits
