I'm no DBA, but I think a database can handle more scripts than you're likely to use. That being said, I think it's best to set up one DB per application to make backing up and restoring much easier.
To clear out a database, use phpMyAdmin and select all tables, then Drop them. Most applications will rebuild the database. If you want to clear out the data from the tables, you'll have to go into each database and select all rows, then delete them.