I always have bought Geomag as it's the best quality. DSs do have some Magnetix and the rods and balls are larger than Geomag so, although they work, they're not 100% compatible.
What about Supermag? I wouldn't bother with it but I saw a Tardis set in Toys R Us last week and DSs would love it! I don't want to get it if it's a different size to Geomag.