You can see articles from this past May and June where high school players signed with D1 programs for this current fall semester (2008).
Schools may show baseball interest after or during your senior season, and those choices will still be available even if you haven't already applied.
I know from experiences with high school players from other sports, that if the coach wants you, they can get you in after the admissions deadline.
My suggestion is to apply to the schools you are interested in if you weren't going to play baseball, plus any baseball schools that have shown real interest in following you at this point. The application is a way of telling the baseball coaches who already know you that you are seriously interested in their school. I wouldn't apply to every school out there.
Applications, even if you use the Common App, are expensive and require fee payments, and often school specific supplemental applications. It does you no harm to apply to many schools, although it's expensive and time consuming (application fees, high school transcript fees, fees for sending test scores, etc.)