If your commute truly has alot of glass and other road hazards, consider putting a good set of commuting tires on your list, such as http://www.bicycletires.com/pmic26/m...26_inch/pp.htm on a budget or http://www.bicycletires.com/pscmp6/s...26_inch/pp.htm or http://www.bicycletires.com/pcocug/c...6_inch)/pp.htm if you want the best.

A good set of tire levers such as http://www.jensonusa.com/store/produ...ire+Lever.aspx

As far as inflation goes, I personally prefer the reliability and lack of waste that a frame pump (or good mini pump) provides versus the more convenient (but higher waste/anxiety - "is there enough air left?") CO2 type fillers. http://www.bikeman.com/PU1105.html

A good multi-tool is a necessity if you know how to do your own maintenance...... http://www.jensonusa.com/store/sub/116-Tools.aspx?s=735

As far as a bag goes, I'd just use a backpack for now, then switch to a rack and trunk bag/panniers long term. Seat bags CAN carry the essential toos, tube, etc, but I personally feel that the money is better spent on other stuff at the moment.

Lighting is worthy of an entire dedicated thread. For a rear light, the PB stealth and Superflash are great values for the money.
Up front, I like to have two lights - one blinking light to get attention, and one for illuminating the road. The latter will cost ALOT of money ($100+) if you want to get a good quality light.