Our server calls stored procs from Java like so - works on both SQL Server 2000 & 2008:
String SPsql = "EXEC <sp_name> ?,?"; // for stored proc taking 2 parameters
Connection con = SmartPoolFactory.getConnection(); // java.sql.Connection
PreparedStatement ps = con.prepareStatement(SPsql);
ps.setEscapeProcessing(true);
ps.setQueryTimeout(<timeout value>);
ps.setString(1, <param1>);
ps.setString(2, <param2>);
ResultSet rs = ps.executeQuery();