Approach

I wrote a benchmark program to evaluate different implementations:

1. instanceof implementation (as reference)
2. object-orientated via an abstract class and @Override a test method
3. using an own type implementation
4. getClass() == _.class implementation

I used jmh to run the benchmark with 100 warmup calls, 1000 iterations under measuring, and with 10 forks. So each option was measured with 10 000 times, which takes 12:18:57 to run the whole benchmark on my MacBook Pro with macOS 10.12.4 and Java 1.8. The benchmark measures the average time of each option. For more details see my implementation on GitHub.

For the sake of completeness: There is a previous version of this answer and my benchmark.

Results

| Operation  | Runtime in nanoseconds per operation | Relative to instanceof |
|------------|--------------------------------------|------------------------|
| INSTANCEOF | 39,598 ± 0,022 ns/op                 | 100,00 %               |
| GETCLASS   | 39,687 ± 0,021 ns/op                 | 100,22 %               |
| TYPE       | 46,295 ± 0,026 ns/op                 | 116,91 %               |
| OO         | 48,078 ± 0,026 ns/op                 | 121,42 %               |

tl;dr

In Java 1.8 instanceof is the fastest approach, although getClass() is very close.

Several tips:

1. Put inserts/updates in a transaction.
2. For older versions of SQLite - Consider a less paranoid journal mode (pragma journal_mode). There is NORMAL, and then there is OFF, which can significantly increase insert speed if you're not too worried about the database possibly getting corrupted if the OS crashes. If your application crashes the data should be fine. Note that in newer versions, the OFF/MEMORY settings are not safe for application level crashes.
3. Playing with page sizes makes a difference as well (PRAGMA page_size). Having larger page sizes can make reads and writes go a bit faster as larger pages are held in memory. Note that more memory will be used for your database.
4. If you have indices, consider calling CREATE INDEX after doing all your inserts. This is significantly faster than creating the index and then doing your inserts.
5. You have to be quite careful if you have concurrent access to SQLite, as the whole database is locked when writes are done, and although multiple readers are possible, writes will be locked out. This has been improved somewhat with the addition of a WAL in newer SQLite versions.
6. Take advantage of saving space...smaller databases go faster. For instance, if you have key value pairs, try making the key an INTEGER PRIMARY KEY if possible, which will replace the implied unique row number column in the table.
7. If you are using multiple threads, you can try using the shared page cache, which will allow loaded pages to be shared between threads, which can avoid expensive I/O calls.
8. Don't use !feof(file)!

I've also asked similar questions here and here.