For the bike, focus on things that can't easily be changed later. Recommend a frame that will easily take a rack, fenders and wider tires, even if you don't install them right away. Also recommend a frame that will take disc brakes for all weather commuting. Style of bike (road, hybrid, MTB) should be thoroughly researched, and it is a good idea to test ride several types of bikes to see what you like. If you have a secondary use for the bike, such as road riding, trail riding, shopping, etc., this will help guide your decision.

Other than that, plan on spending a lot of money on accessories and clothing. Savings from bike commuting will easily pay for everything over the long haul. I used to buy cheaper stuff, such as inexpensive lights, only to find they really weren't up to the task, so try to do it right the first time.