The major difference would depend on food you use to make your homemade baby food. If it is conventionally grown vegetables, fruit, or grains than you are still using foods grown using chemicals and pesticides. If it is important to you not to have these things in your food, then purchase organic foods to make your baby food out of.
Most organic, commercially-prepared do not have the sugars and added ingrediants of conventional baby foods. If the environment is a factor for you, consider that commercially-prepared foods require additional processing, shipping, and packaging compared to making it yourself.
Also, make sure to do your research on the "organic" claims that large companies make. Sometimes they just say it's organic so they can charge more when it is really not. Case in point - see this article from the Minneapolis Star Tribune regarding Target store brand "organic" milk.