My husband is planning on doing the same, and just make sure we don't salt to it etc before pureeing or mushing it up. There should be a lot of information available about this online and other places, (pamphlets on health stations, or hospitals maybe? Books..) to get some basic guidelines to follow.
The jars need to contain additives to give them longer shelf lives, and a lot of nutrition might get lost in the needed processing of the food (for it to be safe for storage), and then they add extra vitamins etc to that instead, to make up for the loss of the processing. (for instance raw vegetables are healthier than boiled vegetables, in a jar it would be boiled to death, make it yourself and you can steam it, bake it, or at least if you boil it not boil it until it's too soft).
I would say freshly mushed food would probably be both tastier and healthier for the baby (just like microwave meals are not as healthy for us as the exact same meal made from scratch at home would be).
Honestly, when it comes to babyfood in jars I think it's used so much mostly because of money, (the people selling it) and convenience (the people buying it), not because it's better for the baby.
We'll probably do a bit of both, as I'm guessing we won't always have time to make his food, or maybe we want to eat something we can't just mush up, and then we can have some bought baby food, but I'm hoping we'll keep that to a minimum.
This is of course only my personal opinion!