Here's an idea of how to add comments to 'Likes', I don't know if it's implementable but here goes...
When you like a comment, a pop-up window appears. This window is basically just a 'Start a conversation' page, but a few fields are already filled in for you; firstly the recipient field is the person who's comment you've liked, the title would be something like: 'cbrads likes your comment!' (for example) and the comment that was 'liked' would be quoted in the text field. It would then just be a case of typing a few words in relation to the comment and then hitting 'Start Conversation'.
If you didn't want to comment, the pop-up could just be closed. The whole 'Comments on Likes' feature could be enabled/disabled in the preferences.
Thanks all for your comments about the likes functionality, I was also disappointed to learn it wasn't an out-of-the-box feature of Xenforo. It was probably the only real thing missing from the migration. I know that the Xenforo team are planning an enhancements to the Like functionality in the next version due out any day/week now; it still doesn't offer the comment functionality as far as I'm aware, but it allows you to choose a reaction (think emoticons) rather than just a like. The conversation functionality that @cbrads mentioned is pretty cool, think private threads on the fly, it could work to integrate it with likes (thanks for outlining your idea), but it'd require some custom work to get it done. For now I'd like to keep things as close to the core software as possible, so in future we can keep it up to date and not fall behind as we did before with Vbulletin.
The story goes back quite a few years @NVP, when Steve was in the driving seat and drafted the Community Constitution and Vendor Policies. They're still there via the Help link in the footer. I need to review them because they're now out of date, and we're not even following our own rules. I've also recently taken a harder line to members posting on the site, and that isn't reflect there. If I feel a member is posting fluff in order to increase their post cost, when really they're really only here to mention a particular broker, product or service, then I'm banning their account and deleting their posts. So if you read a post and suspect this is what's going on (you can normally tell quite quickly from a cursory glance at their recent posts) then please report it using the icon on the post.