Factom is different in a number of ways. PoE hashes single files and records the hash into the Bitcoin Blockchain. You could log many files if you wanted to, and only reveal the files you wish at a later date.
PoE only hashes a single digital thing per Bitcoin transaction. Factom combines many entries together and places a single hash into the Blockchain every 10 minutes. Even if thousands or even millions of entries were placed into Factom, only the fixed entries are placed into Bitcoin.
Factom allows whatever data you like to be hashed and secured. So the data entered and maintained by the Factom network is more flexible.
Factom is way cheaper. PoE charges 5 mBTC to log an entry (~$1.46 at the moment). Factom would cost roughly ~$0.001 to record an entry. That's because everyone using the system is "sharing" the Bitcoin entry.
Proof-of-existence charges $1.50 because he can, and he maintains a servers with a database of all the hashes he created. But, anyone can do the same thing on their own and put a document hash on the blockchain for less than $0.05 - with a small script like this.
Aren't you afraid that if the cost per entry is too low, spam will increase?
Factom combines hashes off chain, and submits a merkle sum tree, so that all hashes can be verified to avoid spamming the blockchain, as at scale which is the hope it would result in huge amounts of data on the chain.
Factom uses federated servers, and incentives to operate to maintain a system as independent as possible. Any other script at scale will cause massive blowback from developers, because of perceived spam. We saw with satoshidice how the limit for dust transactions was upped to reduce their use of the blockchain in their desired way. While it's not an instant result, I would classify what factom is trying to do as the most courteous solution, and scalable, where huge amounts of hashes can be processed off chain, and only one merkle tree is needed per block.