Haven’t quite figured out how to use the spoiler banner so please bear with me.

I presume that in the Justice quest Anders is going to do what he wants whether you help him or not. Regardless of what it actually is that he’s planning (I’ve a vague idea…), how does the outcome change for Hawke if you choose to help or not help (on full friendship)?

My Hawke’s romantically involved with Anders and has generally been supporting him but I really don’t like how he’s being so manipulative over this so might give this one a miss.    

I am currently on my second playthrough and am interested to see how that plays out differently, if at all, since it is kind of a driving event of the tail-end of the game. And be prepared to not like Anders towards the end of the game.

Far as I heard, he is indeed gonna do what he's gonna do in the end no matter what the outcome/choices.
 
Mass Effect did the illusion of choices mattering way better in my opinion, barely anything can be prevented/changed aside from some big things.
Which, in the end, get talked about in general, not even highlighting your decision, often even shining through what the other option mighta been.

Yeah, it's a shame there isn't much you can do, but on the flip side considering what Anders has become by the end of the game, I felt it still worked.

   OK thanks! Now given that he'll still do what he does, if I'm in on it

, will that tarnish my reputation at all or influence my standing with anyone? 
 
@mazik: I already don't like him, the whiny sod. Shame, thought he was kinda cool in Awakenings but in DA2 he just needs to get over himself (which he won't I gather).

Helping him doesn't seem to harm your reputation with anyone else.  Your reaction to what he does will, though. That occurs towards the end of the game, and it is pretty clear who approves and who doesn't, so there's no need to worry.

BioWare turned Anders into a bisexual whiny emo douche. I want sarcastic Anders back.
 
On a side note: Why are all the romances in this game bisexual? Just seems lazy to me.