Dark Empire is a dramatized retelling of canon events passed around in-universe, a thread.

Obviously, Palpatine surviving and returning through decaying cloned bodies. Killing his spirit for good takes a fatal toll in both stories.

In both Dark Empire and the sequels, Palpatine seeks to return through manipulating a Solo child from birth. In Dark Empire, the child is named after Anakin. In the sequels, he's named after Obi-Wan.

In Dark Empire, the Galaxy Gun is a new Imperial superweapon capable of destroying a planet from across the galaxy.

The ore crawlers in Rebels are directly based on the World Devastators from the comic, but with a more grounded scale.

Palpatine's non-Sith Force sensitive acolytes that are based in the same place as Vader's castle call to mind the Inquisitors.

In the comic, Luke discovers the ancient Jedi library guarded by an old Neti Jedi Master. In the sequels, Luke discovers the ancient Jedi library contained in an old uneti tree.

Which also isn't to say the Ossus library from the comic doesn't exist, because it does. And Luke did visit it, it's where he found one of the Jedi texts.

In Dark Empire, Luke brushes with the Dark Side, stands down an Imperial walker, and projects himself using the Force.

It's a bit early to say but the series was responsible for bringing Boba back into the post-RotJ fray, something that's looking like might happen again in a few months.

And that isn't to mention any of the iconic aspects of the modern Star Wars universe that were introduced in the series, from Nar Shaddaa to Jedi Holocrons.