I've been reading about using the winged-edge data structure for storing a boundary representation. However, the linked site says that this is one of the oldest data structres for storing b-reps, are there newer better ones?
Secondly, is there an implementation of this in C#?
The datastructure used for a B-rep is very similar to those used for polygonal modeling - you just replace the edges with curves and the faces with surfaces.
The wikipedia page on polygonal meshes has several types listed, including winged edge. Personally I like half-edge meshes. The only thing they can't do well is non-manifold topology, which you may or may not need. If you do, look for radial edge topology.
There's also a freely available B-rep datastructure from OpenNurbs (McNeel, the makers of Rhino). That also gets you file IO, which is nice.