To start off, know what your Fall Cycling Essentials are: a freshly tuned up bike, helmet, bike lights, and other bits to boots.
Bike lights are important for visibility and safety. And it's the law. Cateye makes some of the best I have used to date.
Be noticeable. Reflective gear is a bonus for commuters who need that visibility during rush hour. I've always been a fan of this bicycle helmet bow, little reflective bird pin, and Iva Jean's two way reflective vest.
Dress for cooler days. That means your mornings are going to chill up a bit so wear a light weight, zip up, wind and rain proof jacket that allows ventilation.
On colder days it may be hard for your fingers to pull breaks and adjust gears, take along some bike gloves that allow you to move your fingers but won't overly heat up your hands. Here are some other cool reasons bike gloves are useful.
Arm and leg warmers are great added insulation for colder rides and they add a bonus for functional fashion. Wearing the right shoe wear is also great to keep your lower extremities warm, check out some of these cute boots from Modcloth.
Also, just a little helpful hint: as the cold starts to settle in, your skin will start to dry. Keep hydrated and moisturized. Here are some tips from Refinery 29 to help you get in the know with fall skin care.