It depends on the license. Generally it's fine to sell open-source apps (GPL - the most common license) as long as you include the source code. If the software is under a less restrictive license like the BSD license, you don't even have to include the source. I don't see anything wrong with what this merchant is doing. The challenge must be finding suckers to pay $39 for what they can download for free.
AFAIK you can't not charge for the apps themselves but you can charge for the boxing, cd, tech help, etc. But these guys are selling them for much more than they should be allowed to. OS Disc sells entire Operating systems for much less than anything on that website.
Not true. You most certainly can sell the programs themselves. What you can't do is make changes to the app and sell that while refusing to release the source code for your changes. But as long as you comply with the license, it's fine.