If buying things isn't in the plans for you, I'm also posting links to tutorials and kits so you can make your own geeky gifts.
TARDIS soap by Luxury Lane Soaps - This is a brand new item that will thrill any Dr. Who fan on your list. Don't know anyone who would appreciate a TARDIS? Well. Luxury Lane has a ton of other products: Star Wars themed, video game themed, and soap that is soap-themed. I've tried her soaps, scrubs, and candles and all are of wonderful quality.
Steampunk Dice Set from RPG Shop - No, the gamer in your life never has enough dice. And these dice are droolworthy. If you think these are a little too fanciful, you have tons of options on that site for dice and LOTS of other tabletop RPG supplies. Encourage imagination and gaming!
Fossils! - I've met few people who didn't think that fossils are the bee's knees. They are easy to find, you can spend as much or as little as you would like, and the variety is endless. I know people that collect both trilobites and ammonites. I've had luck shopping with Fawcett Hobbies for fossils. If you can buy them in person, that's the best way to go. If you live anywhere in the west, you'll probably be able to find a store in your area. I feel like I drove past 20 of them on a drive to Bryce Canyon in Utah. Use some sense too, if it looks fake - it could be. Don't be afraid to ask lots of questions especially if you're paying more than $20 for a fossil.
The Last Unicorn perfume oils from Black Phoenix Alchemy Lab - The Last Unicorn by Peter S. Beagle enchanted me when I was younger. Actually, it still does to this day. A beautifully illustrated comic book version of the tale has been released this year. And now, Black Phoenix Alchemy Lab has crafted amazing scents inspired by the story. This is actually just the first of the series. The label artwork is done by the artist of the comic - Renae De Liz. I suggest buying the perfume oil and giving it with a copy of the book.
Laser Star Projector from ThinkGeek - Who wouldn't want this in their bedroom? No one I know. I mainly included this so that I could say - buy anything from ThinkGeek. They have an amazing selection and great customer service. The end.
Books and comics! The careful choosing of a book for a friend has been a perfect solution sometimes. I've picked my favorites and given them out, this year I'm giving a book that collects the work of a friend's favorite comic book artist, etc. Even if a person isn't a reading fanatic, there might be a giant photography or coffee table book that they will love. If you are friends with a geek, chances are he or she loves reading though. You almost can't lose.
Fountain pen - The timeless quality of a fountain pen is not going to be lost on most geeks. Especially if they're writers. I have a vintage treasure that is pastel peach, and though I do not use it everyday, it gives me a little joy each time I pick it up. I love having bottles of inks and the smudges. And I bet I'm not the only one. Plus it's a gift that has lots of accessories - you can create a whole package with various inks, nibs, and paper. It's another gift where you can spend a whole range of money. The Fountain Pen Hospital is a good place to start.
Finally, I think you should make it a goal to buy at least one thing from an independent artist this year. Check out Etsy and Artfire. There is PLENTY of geeky art and awesomeness and toys on both sites to keep you flipping through pages for hours.