That's really pretty much a matter of personal preference, as long as each of your applications have a distinctive "prefix_" for the table names that might be duplicated (ie. users, etc.).
While most modern applications use such a scheme, there are some that don't and if you put their data in the same database as another application, you can have table name conflicts where one application's table overwrites another's.
On DreamHost, since you can have as many databases as you want, many like to use a separate database for each application just to keep things "sorted", while others like to ease moving things around by having all their applications' data in a single database.
I prefer to keep most applications' data in a database of their own, though I will occasionally share a database between applications - it really just depends on the applications involved, the "prefixing" issue I mentioned, and how many tables the applications use.
PhpMyAdmin can be "slow" and more difficult to use if the database grows to have a huge number of tables. Back in the days when DH only allowed a single database, I at one time had over a dozen applications' data in a single database, and that was a drag.