You'd think that a six-fingered sword would belong to a six-fingered man, but you'd be wrong, because it's Inigo Montoya who hangs on to this sword. The story behind this sword goes back to his father, a master sword-maker who made this weapon for a six-fingered nobleman who ended up killing him. So right away, the sword represents Inigo's father and Inigo's loss of his father.
Inigo has spent his entire life practicing with the sword and learning to fight, in hopes that he will one day track down the six-fingered man and murder him with the very weapon that was made for him. The sword also, then, represents how haunted Inigo is by the loss of his father, and how governed by his obsession with revenge his life has been.
The sword, as we're told, is a beautiful piece of craftsmanship:
How it danced in the moonlight. How glorious and true. Inigo brought it to his lips and with all the fervor in his great Spanish heart kissed the metal… (5.230)
Insofar as the sword is a stand-in for Inigo's father, in its beauty we can see the beauty which Inigo sees in his father. After all, he isn't trying to avenge the death of a tyrant—he seeks revenge in the name of righting a wrong against a humble man.
When Inigo finally uses this sword to kill Count Rugen—a.k.a. the six-fingered man—it's so satisfying. It's been his mission for so long, and he finally accomplishes it. After hanging onto the six-fingered sword all these years, he is finally able to use it to loosen his grip on his father's death and begin to move on in his life. That's poetic justice if we've ever seen it.