What you're desribing is the Eternal September[0].
There are strategies to mitigate the degridation of discourse, such as Hellbanning[1]. Are you asking if there is a way to prevent a small community from blowing up? Or are you asking if there is a way to prevent a small community from blowing up and being bogged down by crappy content?
I would say the best strategy would be to have good moderators, and be sure that you do your part to post quality content to the community. Be the change you want to see online. The more quality content, comments, etc. are on a site, the more it will be socially unacceptable to RickRoll[2].
Many sites implement a karma-type system to reward good content and punish bad conent (Reddit, HN, StackOverflow, etc).
However, two online communities come to mind that don't seem to have suffered in quality of content since their inception: 4Chan and C2Wiki[3]. I think this is due to their obscurity from the mainstream and also anarchist nature of their moderation system. On 4Chan, anyone can post, and there are so many posts, anything untasteful to the community is quickly buried in newer or more popular posts. On C2Wiki, anyone can edit, and edits that degrade the quality of the content are replaced just as painlessly with better content. Interestingly, both communities are anonymous.
How can you prevent people from cracking the same tired jokes again and again? Answer coming in 3... 2...[4]
I think first you must create an online community that caters to a specific niche, so users can already relate to one another because they share the same interests. Once people relate to one another, they want to share and converse[5].
Then, if the community grows in popularity, you must figure out how heavily you're going to moderate. Will you agressivley close off-topic posts and potentially turn away quality contributors (like programmers.stackexchange.com)? Or will you let everyone in, and create specific areas for new interests the community develops as it grows (like 4chan.org/sci)?
I see this a spectrum from razor-focused discussion to organic free-for-all. A mistake I belive one mistake that Slashdot made (and is still trying to rectify) is to straddle both ends of this spectrum. They have ended up alienating both the razor-focused users and the free-for-all users and all that is left is the snark.
So, I think, to prevent the degradation of online communities, you must chose which end of this spectrum your community is on, and moderate (or don't) accordingly.
[0]https://en.wikipedia.org/wiki/Eternal_September
[1]http://www.codinghorror.com/blog/2011/06/suspension-ban-or-h...
[2]Was going to be a YouTube link, but resisted the temptation to RickRoll HN because I might get downvoted.
[3]http://c2.com/cgi/wiki
[4]I'm really tired of this joke on HN, FYI
[5]http://www.browncafe.com/forum/ (one of my favorite niche online communities)