Every situation has its advantages and disadvantages, and working at home is no different. On one hand you can start your day wearing pajamas and you can work any hours you want, as long as you meet your deadlines, on the other hand you're working home alone, missing out on social interaction you would normally have in a crowded office. Trying to decide whether working at home is more on the positive or more on the negative side, though, is pointless, and you'll be better off enjoying what you like about it and counteracting anything that is not all that good.
Not having to rush to the office dressed up in a suit each morning definitely seems like a nice option. You can skip the alarm and get up when you're ready, sit at the computer with crazy bed hair and check your private mail before opening your business files. When you have an errand to run you can take a break because you can get back to the computer after dinner and stay on as long as you need to. Unfortunately, picking your working hours can affect your sleep pattern, and if you spend half the night sleeping and half the day working your melatonin production gets interrupted, interfering with proper hormone balances. That's why even though you can work when you feel like it, you should still try to keep a classic schedule of working during the day and having evenings and nights to yourself.
Most at home jobs require long hours in front of the computer, which tends to negatively impact your sight and back. When working in the office you can run out to a different department or go out for lunch to get some movement, but in the house, where everything is within reach, you don't have that motivation. But you need to make yourself move regularly. Whether it's to take the dog for a walk or to do a quick stretching set in the back yard, make sure you give your back and hands, especially wrists, some release, and that your eyes look at something more than the bright screen.
Working at home requires some extra discipline, and not only when it comes to doing your job consistently and on time, but also when it comes to eating. Since the fridge is just a few steps away, it's easy to reach in every time you need to take a break from your project. The key is to stay on a regular eating schedule, or you'll end up putting on a lot of weight. Small meals every four hours are a great option, since your body doesn't need a lot of energy at once to function properly. Make sure the meals are balanced, that you eat light and healthy, adequately to your sedentary lifestyle, and that you supplement your diet with cholesterol balancing niacin, vitamin D making up for your limited sun exposure and green tea curbing your appetite between meals.
Since you don't interact with people at work, make sure you do that afterwards. Make a standing date with your friends to get out of the house and be with people, find somebody to work out with, instead of jogging alone, consider signing up for a class or joining a hobby group to do something you like with others. That way you won't be always alone and you won't feel like your job is keeping you away from people, letting you enjoy it more if you don't have too many reasons to complain about it.