I use UGCs mainly for loose Nintendo and Genny products, not HuCards. However, one time I did make a "box" using a UGC and put my extra copy of Cadash with case and manual in there. It's kind of funny that the UGCs are designed to fit a CD case as well.
For storing HuCards I would recommend DVD or Nintendo DS cases, and then sliding the game underneath the tabs originally designed to hold the manual. The Cover Project came up with a couple good ways too, and using modified CD cases like others have mentioned works as well. Personally, all my loose Hueys just sit in a stack on the table in sleeves. That's the most protection I really needed since it keeps the dust off the contacts.
As for using UGCs to store other games, while they take up a fair amount of space I can totally see the benefit of using them over just stacking cart games like Genesis, SNES, etc. For one, it keeps the dust off of them so you don't have to worry about the games getting dusty and musty and sunfaded, just the cases which are easily replaceable.