Pinboard's founder seems (understandably) a little unsure as to the future of that part of the service:
"I am optimistic that Twitter will clarify their terms of service with regard to personal backups. In 2012, it remains impossible for a Twitter user to do a full export from their Twitter account. The only way to effectively store and search tweets is through third-party sites."
Founder of Kippt here. We also pull in links from favorited tweets (not all but should probably add that as well) but unlike Pinboard we don't save the actual tweet content, only links referenced in tweet. New API terms are a bit unsure and I'm interested to hear about Twitter's reply to Pinboard.
It's definitely confusing. I'm not sure what the best strategy for tweet archiving is. They might cut Pinboard off at some time, and they might disallow services that post on your behalf like Buffer.
Co-Founder of Buffer here. Great discussion, I hope I can clarify on the Buffer part. The key difference to the way Buffer + Kippt are working is that Kippt pulls in these updates before they are posted. So it is essentially an interplay between people adding updates and Kippt pulling these before they even hit Twitter and Facebook. Hope that clarifies.
Pinboard uses the Twitter API to fetch all your tweets, but as far as I can tell Buffer is not going to see anything you didn't use Buffer to post.