First, think price. I don't know your cash status so I'll try to give a few generic suggestions.
1. The cost of the bike is just the first investment. There are other things to purchase:
Bike pump, tools and/or toolkit, extra tubes, lock, rack and pannier bags/or back pack, lights, helmet, gloves, cycling clothes. Not all are mandatory, or even necessary, but mostly a good idea.
2. A good commuting bike can be road, hybrid, or MTB. I prefer a MTB with 1.75" slick puncture resistant tires with NO SUSPENSION. Suspension adds weight, complexity, and price. Check the Commuting section for additional suggestions and examples.
3. Department store bikes are usually lower quality, but you can make them work for commuting. Please avoid full suspension models in department stores. They will usually fail within the first year of use. Avoid gimmicks.
4. Local bike shops (referred as LBS's here) are hit and miss. They are like finding a reputable auto mechanic (one that won't lie to you at every turn). Word of mouth helps. Buying from an LBS will be more expensive but they (the good ones at least) will fit you properly to a bike, and help you with information.
5. You get what you pay for. Don't expect a $100 bike to last you forever, but if that's all you have (and I would understand), then you can make it work.