These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Batgirl 2009
Epileptic Trees: Her son at the end of the series is Tim's due to his black hair. Heck, some even speculate it might be Damian's!
Steph mom's mentioned that a girl with superpowers and a guy calling himself 'Dr. Mid-Nite' saved her life from Black Mercy. It's a well-known running joke in fandom that Tim resembles Dr. Midnite's in his new Red Robin costume (Steph even calls him out on it in canon). So... was 'Dr. Mid-Nite' actually Tim instead, saving her life discreetly, or was it actually Doctor Mid-Nite himself? Given Supergirl's superspeed, she could have gotten to either one of them, but given Steph and Tim's relationship, and the fact neither Kara or Steph have ever really interacted with the real doc, its a good chance it was Tim.
Fanon Discontinuity: The ending in the final, 24th issue practically encourages this treatment for the following reboot Batgirl series featuring Barbara as Batgirl.
When one of Barbara Gordon's male students sends a text message to Jen, the girl siting next to him in class, commenting that Barbara is hot, Jen clutches her phone to her chest and says "Yeah, she is."
Supergirl: "Aren't you gonna...you know..." Batgirl: "Not unless you wanna see my bra." Supergirl: "Does it have a bat on it?"
It goes way further than that depending on how much between-the-lines reading you want to do. At the end of the issue, as Kara's saying she needs to go, Steph playfully asks "Please don't leave." The next panel is tagged "a few minutes later," and features Steph coming downstairs, her hair slightly more messed. When her mom asks her if she and her friend had a good time, Steph grins and says "the best" as we see Kara's exiting blur through the kitchen window. How'd they spend those "few minutes," I wonder?
After Wendy Harris begins to assist Oracle and Batgirl as Proxy, she begins to hallucinate seeing her dead brother Marvin, who tries to coach her through her physical and mental recuperation. Both Wendy and "Marvin" are pretty clear that this is a manifestation of Wendy's subconcious, not some sort of ghost or hologram, so when Marvin comments on how hot Barbara is Wendy can not help but wonder at what that says about herself and her mind.
Replacement Scrappy: While this largely faded over time, her replacing Cass was not well-received at first, since Cass had already ate it due to Adam Beechen royally screwing up her character. The sole good thing to come from that was that Bruce Wayne adopted her... Then apparently died in Final Crisis, and Cass was Put on a Bus. While Stephanie is popular among Cassandra Cain fans, the way she was replaced did not endear her to many of Cass' fans.
Win the Crowd: Started off strong and kept going from there. The trades are still often bought at stores and fans are still itching for Steph to return.