Is there any way to respond to reputation comments as I feel it a little unfair that if someone writes a comment about a post I have made that I feel is unjustified that I can't respond to it (unless I am missing something)? Or even a way to dispute a negative mark and comment?

At the moment not. You may try to continue discussion in thread where you received bad reputation to explain why did you chose the answer as you did.

I thought about that but then thought it unfair as would essentially be hijacking the thread. Oh well I will just have to fume in silence (there are only 2 comments and both ridiculous but just felt I would like to respond to them if I could).

You could PM the commenter. But be careful. Don't do it too often.

Not much point I don't think as they can't remove their reputation comment

If you say so. Although they might be able to explain why if you are unable to grasp the comment. Or they could give good rep to counter the bad if you're argument is sound.

And if you go through the right channels, the rep can be reversed/removed.

WaltP - you make a good point, thank you. Can I just ask what you mean about going through the right channels to have it reversed/removed? Are you suggesting I contact Daniweb administrators directly?

First is contact the person to understand why.
If you still disagree, flag the post as bad and explain why you want a change.

I can't flag the post as bad as it is not a post it is a reputation comment. It doesn't matter, I just wanted to know if I could dispute or not and it appears not and even if the person who made the reputation comment comes round then they can't retract it anyway.

I can't flag the post as bad as it is not a post it is a reputation comment.

You can always PM a moderator or admin with any concerns. We won't bite, I swear. ;) But as far as reputation goes, it's inherently subjective, so we'll typically not retract rep unless the comment breaks Daniweb's rules (eg. it's offensive or obscene). But it never hurts to ask.