1. Nagios stores it in text files in the log directory, unless you have Nagios database extensions
2. Sort of. I believe Nagios 2 accepts general database plugins which can store the data elsewhere in a database. Here, I have a homegrown utility that parses the text log files regularly and uploads the data into mysql for reporting.
3. Once it is in a database, you can do anything you like with it. I have a program I wrote here that uses either the text files (slow) or the mysql database (fast) to generate availability reports. I'd suggest looking on http://www.nagiosexchange.org
for more third-partyy stuff.