People appear to have been sending very large numbers of addresses dust as a way to break anonymity. Granted, they also may have been doing it as a way to get signatures from scriptPubKeys due to the 'R' re-use issue, but the script would use bitcoind to spend the dust which is known to not be vulnerable.
Also there's lots of pretty much unspendable dust out there from Satoshidice and others, and again such a script can help.
Check with Peter Todd before using (not sure if up to date exactly because was last updated November 2015) but, this could be useful if you are trying to deal with some dust issue (Core)
https://github.com/petertodd/dust-b-goneI also happen to think that dust isn't as big a deal as people think it is. It is a gift, not a curse, and it should be treated as such, people just haven't been innovative enough yet to address it well or meaningfully. See project referred to in my signature.
Also, see BlockCypher's API
http://dev.blockcypher.com/#microtransaction-api(I do not work for BlockCypher, but I consider their work innovative)