First off, you should decide on whether or not you are using a base or editing a vanilla rom. Bases will save you a lot of time, but can be kinda dodgy at times.
Aside from that, Here's my checklist when I'm editing a romhack
[] Moveset changes (for every puppet)
[] TMs/HM changes (if you want to, some bases don't really merit TM/HM changes)
[] Map edits (includes encounter edits)
[] Trainers
[] Item changes (not mostly needed, but mainly used to alter prices and occasionally for TM editing)
[] Scripts (kinda goes in with map edits)
[] Pokedex entries (optional, but adds some flavor)
[] Egg moves (again, optional, but this can break if you have the day-care in the maingame and unedited)
[] Stat Edits (for the puppets.)
[] Sprite Edits (also for the puppets.)
[] Icons (guess.)
[] Evolutions (I'm going to stop explaining the obvious ones now.)
[] Type changes (Any changes to the type chart. Again, optional, but there are tools and tutorials to change how the type chart works.)
[] Trade changes (again, minor but adds some flavor. you don't want a parsee called MIMEN, do you?)
[] Attack Changes (be aware that some attacks in 1.8 use custom routines like charge beam.)
That's generally my list for when I'm editing romhacks, but that's mainly just a start.
