Why don't you run SEOMoz's keyword competitiveness tools to get an idea of what makes them better. Also, take a look at some competitor data sets like Majestic and AHrefs - I always start with SEOMoz, but there is no reason to limit yourself to 1 data set. Chances are they have a bunch more spammy links that you aren't yet seeing, and those are giving them the lift.

I wouldn't worry about it. Your site is indexed in Google and is, likely, cached. Just because Google's cache: operator isn't working properly for you at the moment isn't a real cause of concern.

I have never seen any evidence that commas are negative, however usability can often drive the social factors that may play more and more a role in the future. I wouldn't make it a priority to change those URLs now, but when the time comes (perhaps with a redesign of the website), it would be worth your while to go ahead and remove them.