Ever since they first started cracking down on throwing inside (pussies), most of the time umps have issued a warning after the first HBP (unless it was very obviously malicious and/or caused injury) and ejected everyone who plunks a batter after that point, unless it was very obviously a pitch that really did get away from them. And that really isn't that hard for me to believe anymore.
More and more guys are trying to cultivate harder sliders and bigger slurves after seeing the success those quicker breaking balls have brought to guys like Roy Oswalt or more recently Daisuke Matsuzaka, but not everyone has the chops to keep said pitches under control. Many a B-list or below righty has hit lefty pull hitters (who frequently crowd the plate just a little to get ahold of stuff away), and vice versa, because they haven't spent enough of their bullpen sessions on breaking balls to iron out their mechanics. There's milliseconds of timing and infinitesimal nuances of muscle memory involved in painting the corner, and a lot of the time you'll see tired starters or cold relievers just lose track of their release point.
Anyway, it's really easy to jump the gun (ESPECIALLY with BoSox/Yankee$) and assume every HBP or near-miss is intentional, but it isn't always. Pitching is always at a premium in baseball, and a lot of guys who get called up are under so much pressure to perform that they sometimes throw pitches they haven't polished enough to use at this level yet. It's easy to think that your favorite player on your favorite team was plunked intentionally or thrown at intentionally, and sometimes umps jump to the same conclusion. Just my two cents.