Is there a quick and dirty way to detect all transactions whose tx-id can be found in more than one transaction since the genesis block?
There are multiple ways to read your question.
Are there cases where the same transaction has been included into the blockchain multiple times?
Yes. There is one recorded instance of the same coinbase appearing twice. The problem this causes is that only one of these can be redeemed. It also makes it possible to reduce a fully-confirmed transaction to one confirmation, though I don't understand the details. BIP34 fixed this.
Are there cases where the same input hash appears in multiple transactions?
Yes. It happens all the time. For example, transaction 9fa3... has two outputs. Those two outputs were spent by two different transactions. Each transaction needed to include the same input hash (though the vout field was different.)
Are there are any known collisions in SHA256?
I would also like to see mutated transactions as well although I am not sure if the blockchain keeps a historical track of the mutated transactions.