Thanks for the comment, Jennifer. I agree with this:

If the abstract justification falls away, the justifications can sound hollow, and the practices can stop with negative real world consequences.

To your two examples, I'll provide two responses.

Re. Prayer: Given that I suspect god doesn't exist or is probably non-interactive to say the least, I'm put in the position of needing to re-evaluate what really was occurring to transform my life. Obviously something occurred which transformed me from someone who resorted to substances during emotional lows to someone who no longer even feels that urge. I have also been able to quit smoking (which I found far more difficult) and have not had a cigarette in 4.5 years. But what was it?

My current theory (extremely rough) would propose that for believers, "god" represents "that which is perfect" or a moral watchdog of sorts (again, rough... just play along if possible). Meditating on what "what is perfect" would dictate you do with your day and time could be quite helpful. Dan Ariely shows that even when atheist swear on a Bible they are less prone to cheat afterward. Reflecting on "the good" (for believers, god's will) probably produces tangible results.

As such, I have definitely thought of taking up a morning meditation/reflection ritual of some kind. I've not done so, which probably shows that somewhere in there meditation isn't yet worth the extra snoozing I do each morning, but I can at least state I think this would be a valuable replacement for my former practice of prayer. In essence, I think I'm really going to be doing something similar... it's just that now I'll see it as what it always was: self-reflection on the best approaches toward various situations and how to self-improve rather than thinking that asking a non-existent being for the strength to do so was actually doing anything at all.

As a related one... I was in a men's small group with fellow Catholics where we would discuss how god was working in our lives, what we were struggling with, etc. This, too, I think is a helpful practice and would fall into the category of things that have been thrown out by me, currently. It is one like prayer, though, in that I'd like to find a group of individuals interested in discussing life challenges and methods of "remedying deficiency" (as I like to call it). I have not found such a group quite yet but suspect that LW-ers may have something like this or that perhaps something like this can come out of my local Minnesota Atheists group.

Re. AA/12 Steps/Sobriety: This one is more interesting to me. At a point in the past, you're probably right when you say that shedding my belief in god would have made my sobriety precarious. Part of this, however, is how AA teaches one to think about the nature of alcoholism. Here are some quotes to illustrate my point:

For when harboring such feelings we shut ourselves off from the sunlight of the Spirit. The insanity of alcohol returns and we drink again. And with us, to drink is to die. (Alcoholics Anonymous, 4th ed., pg. 66)

We alcoholics are men and women who have lost the ability to control our drinking. We know that no real alcoholic ever recovers control. (ibid, pg. 30)

God is doing for us what we could not do for ourselves. (ibid, pg. 84)

The theme is that of permanent sickness coupled with the dictate that only a "power greater than yourself" can restore you to sanity. AA's common message is that this power can be anything, even a chair or door knob. But when reading from the chapter entitled, "We Agnostics", note this passage:

Imagine life without faith! Were nothing left but pure reason, it wouldn’t be life. But we believed in life—of course we did. We could not prove life in the sense that you can prove a straight line is the shortest distance between two points, yet, there it was. Could we still say the whole thing was nothing but a mass of electrons, created out of nothing, meaning nothing, whirling on to a destiny of nothingness? Of course we couldn’t. The electrons themselves seemed more intelligent than that. At least, so the chemist said. (ibid, pg. 54)

I take this to mean that AA directly advocates at least a form of intentional creator god. AA was built with a Christian foundation, even if they stripped most of this away for the sake of universal accessibility. This passage also suggests (to me) an implication of nihilism if such a creator does not exist.

So, what to make of all of this? In my reflections on the steps themselves, I am not sure what to make of the first three any longer. They require an admission of personal hopelessness, that only a [supernatural] power greater than yourself can fix you, and that, therefore, the only sensible decision is to surrender your will and life (the difference?) to such a being. But what if there is no being granting such transforming power in return for submission/allegiance/dedication!?

The heart of the program, I believe, lies in steps 4-10. In summary, they are to "take inventory" (make a list of wrongdoings and character flaws), and discuss these findings with another (steps 4 and 5); to become willing to have such shortcomings removed (steps 6-7); to make a list of those you've harmed and to amend the relationship (steps 8-9); and to carry out a sort of "mini" version of 4-9 on a daily basis (step 10). This begins to sound like a form of reflection and reflection-inspired action which would begin to remove sources of guilt and self-hatred which could very well have been a prime contributor toward alcohol dependency in the first place.

Edited 10/2011: removed what followed. Personal details I chose to delete.