If you got a commercial site selling stuff and there is a section offering freeware this freeware is used for commercial purpose, too, even if it is for free.
Reason?
You use the freeware to get customers to your site which makes the freeware a commercial part of your site.
But I doubt anyone would cry about it.
I even made a application to Squaresoft once, showing my site as example and I got this "Chocobo World" remake there and nobody lost a word about it.
On the other Hand for my (free) browser game "Schlacht um Kyoto" I once recieved a mail asking about the sources/ origins of my images and if self made that I have to own the necessary software licences (of course this was no specific thread since there is nothing "stolen" and thus any answer would be worse than no answer, but there are people earning their money finding people stealing stuff of others).
But even for my game "Starbattle" which uses dozens of images from Namco VS Capcom and Halo Zero nobody cares a f***.
If you just provide freeware downloads on your site nobody cares as long as it does not get too big.