Comments get more upvotes, independent of quality, if they:

• Are in a high-traffic thread
• Are made while the thread is still new
• Get an early complimentary reply
• Make a point many people agree with and care about (especially if the first to make that point)
• Become the highest-karma comment early on (bandwagon + people may only read/vote on the first few comments, so being the top comment is valuable)
• Are closer to top-level (people don't read deep into threads unless particularly interested)

I think these effects, in aggregate, are probably much stronger determinants of comment karma than actual quality. Top-level posts, to main or discussion, suffer from fewer of these effects, so their karma is a little more reliable. But I hope no one is taking their comment karma too much to heart.