FYI to everyone, coming from a D3000 user, yes it has program mode and something call guide mode which is program mode made easy. On a D3000 uping the iso is only good till about 400 after that it starts to grain out fast. The D3000 also has the Active D-Lighting filter that you can turn off and on, it helps with the grain a little, however the write times to the memory card are very long, and you can miss shots because of it. (These are the two reasons I'm getting out of the D3000 at tax time for a D90) I'm not knocking the D3000 it was a great camera for me, and I have taken some great shots with it but I outgrew it even before I bought it, just didn't know it at the time.
I do a lot of dark outdoor night shooting, and find myself shooting in Aperture Mode at f/4.0 - f/8.0 for starting points with 10 to 20 sec exposures (on a tripod) then adjust the aperture from up or down from there as needed. If your exposures start to turn red you need to close your aperture and or shorten you exposure time I run into this all the time shooting lightning pictures because I have to wait for the shot.
As for inside shots not going to be much help here. Stay out of program mode, I find it makes your pictures blue in tint (well at least mine maybe I'm doing something wrong still have to overcome this issue and stay out of program mode) I find the onboard flash is weak in a large area, you might want to think about another flash unit. Flash units everyone has an opinion on that. I don't want to start thread inside of a thread, but I will tell you I heard the SB400 will work better than the onboard flash, however personally as soon as I can get my hands on a SB700 I'll be using that. You'll have to decide what you want and what you need.
In the mean time, now it will not look the greatest but try making a bounce card out of a index card bending it at a 45^ angle and taping in front of your on board flash. I have had a lot of luck doing this with shots around the house.
That's it from me a D3000 user, I'll let the experts take over from here.
Test shots
f/5.6 200 iso
On board flash
Test shots
f/5.6 200 iso
On board flash index card bounce card
Both photo's
Photoshop for personal cosmetic reasons
(Skin cancer removal)