All three sentences are radically different in the contexts in which they can be used. For a full explanation you would need to consult an English grammar. Here are some main differences. I am eliminating the "do" to make this examples easier to understand.
In my previous organisation we would not work much. One day the mailman came with a new package...
Here the use of the 'would' construction indicates that the action described is habitual or continuous. This construction is used when describing persistent background conditions in which other events happen.
We were not working much when the large order finally came in.
Here the past progressive tense is used because "doing" is describing an action that is pictured as in progress at a particular point in time when another action happens. The important part is the fact that it is in progress.
Finally, the 'had' version is less common and usually interchangeable in modern English with the previous tense. However, modern English still strongly prefers the 'had' version when the focus is on the length of time the action has been in progress or the change that is caused by a second, later action.
For example, to paraphrase from Wikipedia,
I had been working on my novel when she entered the room to talk to me.
implies that I stopped working when she came in (or had already stopped a short time before); the plain past progressive (I was working...) would not necessarily carry this implication.
As I said, an advanced English grammar will describe this in much greater detail and precision. Wikipedia has some information here: http://en.wikipedia.org/wiki/Past_perfect_progressive#Past_perfect_progressive