Both iCab Mobile and Atomic Browser (full version) have download abilities. I think iCab's are a little more complete and easier to manage. iCab can also (for a few sites, none of which I have personal experience with) upload from it's own folders.
GoodReader also has the ability to download files, either by entering the URL or through it's built in browser. It's good for this, but since it was designed specifically to go get downloads it tend to be too annoying for regular browsing. It keeps asking you if you want to download when you tap on links.