AFAIK, a transaction must have all outputs above 5460 Satoshi to be considered as a non dust and have nodes relay it.
Wasn't it changed to 546 satoshis after the commit? https://github.com/bitcoin/bitcoin/commit/6a4c196dd64da2fd33dc7ae77a8cdd3e4cf0eff1
Yes, dust is currently 546 satoshi[1].
It is generally a bad idea to use 0 fees for anything below 0.1BTC since the priority would be so low that it would take a long time to confirm.
AFAIK isn't it 0.01BTC which is considered higher priority with zero fee?
The amount alone is not the point. The rule of thumb (aka bitcoin day) is one bitcoin confirmed for 1 day (144 confirmations), thus 0.1 bitcoin would need 10 days and 0.01 100 days or ~ 14400 confirmations to have a high enough priority to be send without fees. Another thing to keep in mind is that no matter how high your priority is, there is only 50KByte in each block reserved for transactions without fee. So there is no 100% safe way to send a transaction without fee. Currently however most transactions pay a fee. I suspect this is due to the changes in bitcoin core (0.10.0) that allow a better estimation of the fee.
[1] https://github.com/bitcoin/bitcoin/blob/df5c246ba38c5b5bdd6192b0201d2fe8245451ca/src/primitives/transaction.h#L140