Speaking in an interview with DS, Allan revealed that she is particularly proud of creating a greater sense of community among the show's characters in recent months.
Asked about the programme's 2009 highlights, she replied: "I have lots of proud moments. One in particular… I'd probably say it was when I received a phone call from one of the cast to tell me how much they were loving the scripts and how pleased they were that their character could have conversations with anyone else in the show.
"That was one of my objectives at the start of the year, to ensure that characters weren't locked into their own stories."
Meanwhile, Allan singled out Newt's (Nico Mirallegro) suicide attempt plot for praise, naming the schizophrenic student's troubles as her favourite storyline of the year.
"The way in which we told that story was so Hollyoaks," she explained. "I know there's been criticism that we've been too teen-focussed across the year but for me, that story held its own."
The programme's boss continued: "My favourite scene of the year has to be the underwater sequence with Newt, Rae, Eli and Jack the hero! It was a beautiful moment on screen and it was the moment that the audience realised that Newt was trying to kill himself. For me, that moment of realisation made that scene so powerful. I must have watched it about 40 times, but it gets me every time."
Allan was appointed as Hollyoaks' leading producer in October 2008 following the departure of her predecessor Bryan Kirkwood. She had previously worked as deputy producer.
> Click here to read Lucy Allan's Producer's Perspective 2009
> Click here to read what's to come in Hollyoaks in 2010