You can map a route from an area of town to a specific address downtown using http://infoweb.sacrt.com/. I agree with Stephanie and Jim; it is difficult to suggest specific areas without knowing more about what you are looking for in a home and your price range. The closer to downtown you get (East Sacramento, Land Park, Curtis Park, etc.), home prices climb. However if you live in an outlying area, prices tend to be more affordable. Different areas also represent different styles of living...
For example, if you are coming from Arden & Eastern - you could take Bus Line 29 at 7:13am in the morning, and be downtown at 7th & H Streets by 7:34am with no transfers. Within walking distance from Arden & Eastern, there are homes that range in price from $305,000 - $1,249,000.
You could try to "reverse" engineer this a bit too. Where downtown are you trying to commute? You could determine what the local bus line stops are, and backtrack what areas those lines stop in.
I hope this helps a little...if you post perhaps some of your home search criteria, we might be able to better assist you.
As a regular bus commuter, it's my automatic and natural response that the closer you are to downtown, the better the commute. However, many communities have bus service that is either direct to dntn or to a light rail station. Commuting in the late evenings can be difficult; if you're working nights and weekends, your commute timeline may be affected.
East Sacramento, Land Park, Curtis Park, River Park and South Land Park have direct bus lines. While Hollywood Park has light rail service. These are areas I've commuted to/from and the trips are relaxing and efficient.
If you break down your price range and home specifications (sq ft/yard side/home style & age), it's easier to identify what neighborhood fits your needs. Take a look at sacrt.com for more information.
Link to RT Map is below.