Although having a nationwide JR railpass (the 7days, 14days, 21days versions) generally covers all trains operated by JR company, with a few exceptions.
Example:
- You cannot take Nozomi Shinkansen on the Tokaido Shinkansen line...although you can take the Kodama and Hikari Shinkansens which also runs on the same line. The difference is that Nozomi's travel time will be faster since it skips alot of stations along the route.
-same with Mizuho Shinkansen on the Sanyo and Kyushu line. You cannot take Mizuho, but you can take the other Shinkansen that are also running on the same route.
- There are some JR trains that runs on tracks that are operated by non-JR companies. In those cases, even though the train is a JR train, but you still have to pay a surcharge to cover that non-JR portion of the journey.
You can see a list of the trains that runs on parts of non-JR tracks on this page:
http://japanrailpass.net/en/about_jrp.html
Although u can use your JR pass to get free seat reservations on Shinkansen and Ltd Exp trains. but remember you'd still need to go to the JR ticketing office before your journey to book your reserved seat tickets using your railpass so that they can give you a ticket with your train and seat number.