Several Magnetix products were marked as clearance at my local Toys "R" Us. I was told they're trying to get rid of them to make room for newer ones.
The prices are pretty low at http://www.toysrus.com, but they seemed lower in-store. I don't know if this is true everywhere.
These were the products I found locally:
150-pc (#2813) $12.48
120-pc Micro (#28287) $4.98
25-pc Special Parts: Colored Balls (#28318) $2.48
17-pc Special Parts: Lights & Bars (#2877) $2.48
85-pc Metallics (#28491) $7.48
85-pc Translucents (#28487) $7.48
Other stores might have other varieties.