Choosing the db as well as writing the ERD should be your priority here. Fortunately, using basic SQL syntax is standardized, so you can get away with changing your mind so long as you don't do anything proprietary. Why not an Oracle database for example? Oracle and Java play along quite well, as does Java an MySQL. I've used Java for SQLServerExpress, but not an enterprise SQLServer. I don't recall it being difficult to set up, but would definitely need a package for it (MySQL used to as well, but now that oracle acquired sun, I'm not sure if its built in nowadays).
Personally, I avoid JSP and Servlets like the plague. I've never had anything but troubles with implementing them, and have always found them to be overall issues in stability. I do like that it is quite fast though.
Its easy to create graphs in both Java and PHP. Personally I'd use PHP if its for a website, and Java if its for a desktop app or applet. If I need to use Desktop and Web app, I'd consider using soap between them.