1) Despite guidelines, people vote up comments they agree with. If they have enough karma, they vote down ones they disagree with. There's little you can do to change such a situation
This is inadequate — sometimes you can see interesting and informative posts up the top; sometimes interesting posts have a relatively low comment score, simply because they are controversial. The more specific and detailed a post is, the more chances they have to offend (or just not overall agreement), and the more chances they have to get a downvote/not be voted on. If a comment is very general, (eg "How awful.") it will be a lot less controversial, and thus more get more votes.
On the other hand, it can be useful to see comment scores as a barometer to popularity — which framework/language/cool solution for a specific problem is upvoted the most can be genuinely useful information.
This is a problem that many sites that implement "voting" have. I'm not entirely sure of what a solution can be. One might be that there be two metrics — one for interestingness/helpfulness/what the guidelines are for anyway. The other for whether you agree with a post(/find it funny). There are potential problems with this idea, for instance, it complicates voting (the simplicity of a vote increasing a comment's score is one that everyone can understand). However, I think that the benefits would outweigh the costs.
2) Comment threads that try to be increasingly funny, with signal to noise ratio decreasing with every increase in depth. I often find myself scrolling down past a lot of uninteresting and unimportant comments to get to the next comment that isn't part of the first thread. This is a little harder to tackle, as sometimes good comments can be revealing deep in a thread full of mediocre ones, making it difficult to just fold comments part a certain level. Perhaps only fold when most of the comments are under a certain threshold (like 5 points)?