It's not shown, but I think Ganondorf kills the King of Hyrule in OoT. Plus the sage in Loz: Tp and he has probably done so in the past.
In Twilight Princess and OoT and Wind Waker it hints at his past which says he murdered many, that being said, knowing the brutal nature of Ganondorf, he probably murdered thousands that didn't go along with his order or his claim of being the true ruler of Hyrule when he was rising to power.
After playing OoT3D I can confirm that the Gerudo woman, Nabooru, mentions how Ganondorf murders innocents. and this is before his takeover of Hyrule.
In the back alley once you get the ocarina of time but before the temple of time in OoT, there is a soldier who is dying and he says ganondorf did it to him. He tells you the message Zelda told him to give to "The forest boy" Aka Link, and sadly, dies. Try to talk to him again and Navi will say he's not moving anymore.
He did lay a curse on the Deku Tree in OoT, which spawned Gohma, who ate away at or otherwise damaged the insides of the Deku Tree, ultimately killing him, despite Link's heroic efforts.
In the Wind Waker Ganondorf murdered the earth and wind sages Laruto and Fado with Jalhalla and Molgera, so Link had to find the next sages- Medli and Markar and killing Jalhalla and Molgera so they became the official sages.
In TP, he kills Midna, but then the Light Spirits heal her and bring her back to life, so...Yes, he did kill people.
Dude, he has killed so many people it's not even funny. I highly doubt that his intentions were to simply take the land of Hyrule because he was envious of its wind.