I would like to port a PHP/MySQL-based client/server application to be a standalone desktop application written in Java. The database has grown to be fairly large, with several tables with hundreds of thousands of rows. I expect these could grow to over a million entries for certain tables.

What embedded database would best handle this? HSQLDB and Sqlite seem to be the obvious choices, though I'm guessing there are others out there as well. My main priorities are the ability to perform queries on large amounts of data efficiently (this thread seems to confirm Sqlite can handle this) and the ease with which I can import old data from MySQL (I remember HSQLDB being kind of a pain for that).

Note: I am aware that similar questions comparing embedded databases have been posted before (for example here and here) but as my priorities differ somewhat from most applications considering the large data migration I thought it justified a new question.