I mistakenly put the auto transmission in 2nd gear and drove my new 2004 Rav4 4wd for about a half-hour without realizing it. Most of it was on the highway at 60+ and the rest was on regular or hilly roads. What kind of damage have I done to the transmission, is there any way that I can tell without taking it to the dealer for a check-up, or does it have to go to the dealer for service and how much might it cost even though it's under warranty?

I doubt you have done damage to your transmission. The engine in your rav loves to rev, and sustained high rpm's are more likely to hurt your engine than your transmission. I run mine up hills on the freeway and about 80 in 4th and no problems.