AMA Superbike, World Superbike and MototGP are probably the 3 biggest series' there are with British and Australian Superbike right behind them.
The 250s of course are powerful 2 strokes. I haven't been to WSB races since the early 90s so I'm not sure if they still run the 2 strokes as support classes or not. They probably do since 2 stroke street bikes are legal there. The AMA stopped running 2 strokes not too long ago. Most US club racing organizations have some 2 strokes running including the 250s and the 125s.
MotoGP championship was all 2 strokes just a few years ago. Now the top bikes are 990cc 4 strokes but the 125cc and 250cc 2 strokes are still big in that series and they produce some great racing.
Yamaha holds its own in pretty much every series. Especially MotoGP.