You all have good points.
There
has to be a reason for why Hermione is the voice of Harry's conscience. JKR isn't one to just throw something like that into the books without there being a reason behind it wheter it's hidden at the time or not.
All that remains to be seen is why Hermione is always in his head/on his mind. The shipper in me is convinced that it's because he loves her on a subconscious level at the moment, but hopefully that'll change soon. Heh.
On the other hand the pessemist in me continues to urge me not to get my hopes up too high right now. There could be other reasons as to why he's always thinking about her.. although what these reasons are, I have absoultely no idea.
Now, as for Voldemort figuring out how much Hermione means to Harry and taking her to hurt him could be a possibility. I mean, how many times has that happened in fics??
Yes, it could happen and as most of you have said it may just be the trigger needed for Harry to wake up and smell the coffee as it were.
Another interesting point I've been mulling over is that "a power he knows not" could well be love as it has been suggested, and perhaps Voldemort discovers just how powerful love can be when/if he takes Hermione.
Now, this is entirely speculation and a complete guess work, but if Voldemort takes Hermione and Harry finally realises just how much she means to him then Harry would obviously do anything and everything to get her back. That could start the "final battle" and Harry fighting to save the woman he loves would most definately be a formidable enemy. With the added power of his love for Hermione Harry could become un-stoppable!
I agree that Hermione being the voice of Harry's is very interesting and possibly very important in the running plot of the books.
Good spotting!

~Bec