From my investigation and reading a lot about this, it seems like the transaction is just removed and the ether returns back to some address. With Bitcoin, orphaned blocks are initially accepted by the network, but will be rejected once a longer blockchain is received that doesn't include the block. Is the same thing true in Ethereum?
According to Ethereum White Paper transactions of orphan (uncle) will be added to the chain anyways.
As described by Sompolinsky and Zohar, GHOST solves the first issue of network security loss by including stale blocks in the calculation of which chain is the "longest"; that is to say, not just the parent and further ancestors of a block, but also the stale descendants of the block's ancestor (in Ethereum jargon, "uncles") are added to the calculation of which block has the largest total proof of work backing it.