Special features are the same on all the sets. There are only two real differences between the initial releases and the subsequent box sets...
The first three seasons came with the extra bonus items (replica notepad, sketch book, & artwork sketches). Said initial releases of the first three seasons also came in a bit more "deluxe" packaging while the subsequent release of the fourth season as a stand alone (ie not in a box set) came in more traditional DVD case style packaging.
There are two different complete series sets.
There's the cave style packaging that was released first. While very neat looking, it's not very practical for storage of the discs. It's a binder style packaging in which the discs slide into paper "pages". Unfortunately this means that the discs often come dislodged and get scratched up. I was lucky with the one I purchased in that no discs were scratched to the point of skipping, but others were not so fortunate.
The second full series release came housed in much more traditional DVD style packaging (like the seperate fourth season) with all four indicidual boxsets sliding nicely into a full color cardboard box. It's the same discs and the same bonus features (minus the replicas that came with the initial releases of the first three seasons) but much safer and much more practical packaging. Overall, I would highly recccommend this set (link below - ignore the low star rating due to Amazon combining reviews for the first and second full series sets, resluting in all the negative comments about the poor packaging on the first release being added to the reviews of the second).
In your case, I would suggest getting the second release full series set and donating the first three seasons you already have to a local library, pre-school, or daycare center (though, you should keep the replicas goodies if you got them as those are pretty awesome).
http://www.amazon.com/Fraggle-Rock-...8&qid=1349482821&sr=8-2&keywords=fraggle+rock