The first thing you'll see when entering the lighthouse is Garnak sitting at a table. He'll sell you a few weak items if you'd like to look at his inventory.
The rooms to the north of Garnak are a library, a book room and a bedroom, but there isn't much of anything in any of them.
The room to the south of Garnak is Elspeth's Crystal shop. Talk to Elspeth and she'll ask you to recover a crystal stolen recently. She thinks that it was the keeper of the Northpoint Lighthouse, but it was actually a horrid spectre who stole it. If you haven't already been to the Northpoint Lighthouse consult my walkthrough to find the location of the spectre and crystal. Once you return the crystal Elspeth will give you a full set of her crystals, consisting of a Recall Crystal, an Unshackling Crystal and a Piercing Crystal, as well as a Fine Crystal. You can buy crystals off of her as well.
The two rooms to the south are storage rooms, and the western of them has a secret passage on the western wall. This secret passage leads out to a little ledge of land containing a few plain crystals that aren't even really worth picking up.
Now it's time to head to Shayder and begin the roach quest, which is already about half done, actually, if you've been doing this in the order shown on my list.