Ned only really lies about Jon's true parentage but he doesn't necessarily lie when he doesn't lie by refusing to tell Robert of his mother or letting Catelyn believe what she does. That's just withholding information rather than lying per se.
That said Ned does lie again when he is forced to "confess" before Joffrey has him executed.
Eddark Stark: I am Eddard Stark, Lord of Winterfell and Hand of the King. I come before you to confess my treason in the sight of Gods and men. I betrayed the faith of my King and the trust of my friend Robert. I swore to protect and defend his children, but before his blood was cold I plotted to murder his son and seize the Throne for myself. Let the High Septon and Baelor the Blessed bear witness to what I say: Joffrey Baratheon is the one true heir to the Iron Throne, by the grace of all the Gods, Lord of the Seven Kingdoms and Protector of the Realm.
Game of Thrones, Season 1 Episode 9, "Baelor"
I count at least a few lies here from Ned's point of view.
"I come before you to confess my treason in the sight of Gods and men." He doesn't believe he is being treasonous in his actions but rather following the rightful procedures for who should be king.
"I betrayed the faith of my King and the trust of my friend Robert." If the King he is referring to here is Joffrey he doesn't believe him to be King so that's a lie. He also betrays Robert's trust but he believes he's acting in his interest so that could be a lie or not depending on how you look at it.
"I swore to protect and defend his children, but before his blood was cold I plotted to murder his son and seize the Throne for myself." He knows Joffrey isn't Robert's son and he wasn't seizing the Throne for himself.
"Joffrey Baratheon is the one true heir to the Iron Throne" He knows this isn't true as Joffrey isn't Robert's son so again a lie.