I started out working on A4, since that was the size paper I always worked on, so it was nice and familiar to me. I've recently switched to B5 size paper though. Main reason being it is almost indistinguishable from A4 in proportions, and after being at a con where there was a lot of different size comics, I found that was the size I liked, considering holding it, and it's transportability. B5 is the size of the Avatar - The Last Airbender comics if you know those. It is a bit bigger and more elongated than takoban (mangas), which are roughly A5 in size. I hope that helped.
I also work with about 1 cm margins.
Also remember if you work digitally to work in minimum 300 dpi (Dots per Inch) of you want it printed!