My Dobe puppy helga (8 m/o) is the sweetest dog you can see, she has zero dominance or aggression. But she has this annoying habit of running upto me and nudging my hand and asking me to pet her. I was a sucker and I kept doing it with out even realizing what was happening. She had conditioned me to pet her.

Over all she is a hyper dog. If she is not getting petted, she will want to play with her housemates, if not she has to chew on a stick or chase a squirrel, once that is done she will see if she can get petted again etc.

Anyway, I have stopped petting her when she nudges my hand, now I am teaching her that she has to come and sit in front of me and wait to get petted. She LOVES attention from me. She will stand still or sit in my lap even for 10 minutes straight if I keep stroking her belly or head and back.

As I mentioned before she has zero dominance or aggression.

BUT, is this behaviour of demanding to be petted also a form of dominance. Am I doing the right thing by petting her , but only after she comes and sits in front of me and WAITS?

I'd say it's more of a learned behavior rather than one of dominance. Like you said, she nudged, you rewarded. Behavior taught.

Have you taught her to settle on command? Since attention from you is such a high motivator you can use that as a reward for settling down.

I think this might be what you are doing, but am not sure: I would totally ignore her demands to be petted. When she's NOT bugging you, call her over and ask her to sit for pets. If you ask her to sit and pet her when she's demanding attention, it will create a chain. She'll think "if I nudge him he'll ask me to sit and then I get pets". You want the sit/pets to be unrelated to her harassment.

It doesn't sound dominant to me. Dobermans are Velcro dogs and they live for attention from their person. She is at an adolescent age so she has no impulse control and is trying to figure out the quickest way to get what she wants. It can get pushy later if it continues, but you are addressing it early.

In my experience, that attentiveness and high energy will likely channel nicely with time and training into speed and focus.