1 - don't spam
2 - really, don't spam
3 - put in some effort
4 - keep it short
More often than not, you're given the chance to bypass the HR filter and get in touch directly with an engineer. This is key. Your default cover letter won't cut it, because engineers look for different things, so you want something tailor made every time. It takes some effort, but this will pay off.Make sure you understand what they do, what they want, and what you can offer. Make sure you (quickly) go through the latter. You probably have something to offer even though you don't fit the profile they had in mind.
Make sure you know who you're writing to, and craft your email accordingly. Google him, go through their HN submissions/GitHub/whatever, get a feeling for what they might like.
Oh, and try to be nice and genuine, at this stage is a lot about people skills :) Good luck!
Honestly, I am really disappointed in how this is handled by them. It appears like they are looking for candidates urgently, but then do not even react. At least I would expect a rejection (with or without reasons given), but I got nothing instead. It was also not the case that I applied for jobs which did not fit my skill set or experience. In fact for most of them my experience would have been a very close fit.