Though The Lion and the Unicorn (1995) was the last episode aired, this was the last episode produced.
The title Batgirl Returns pays homage to Batman Returns. Which has Catwoman as one of the main villains and briefly shows The Penguin who both appear in Batman Returns.
This is the last time Melissa Gilbert voiced Batgirl. She was replaced by Mary Kay Bergman in the direct-to-video movie Batman & Mr. Freeze: SubZero and was later replaced by Tara Strong in The New Batman Adventures.