I like to organize my apps into folders of aliases. I do this by dragging them into folders holding option and command. For some reason the icons are not showing up for the aliases for many applications. Here is a video.
They show up with the Clean App icon: http://www.syniumsoftware.com/cleanapp/
It is a strange issue. Does anyone else have this problem?
Okay - that one worked.
So, the issue is not that icons, the aliased items, are missing per se, it is that the aliases are displaying an incorrect icon.
The incorrect icon appears to be a modified .zip icon. Why that is being used, I don't know unless it is a combination of how the app is written and whether it complies fully with OS X programming requirements. An alias is functionally nothing more than an icon and a pathname. The OS should grab the icon to be used from the resources in the source file. However, if that is miswritten somehow then the OS might grab any icon; for some reason it may be 'remembering' the icon used by the original download for the item.
This happens often with documents (image files, text files, etc.) when aliases are made to them - since what appears to be a custom icon is often a temp one created on the fly by Preview, it does not survive to the alias, which gets displayed with a generic icon.
One thing you can try to see if it will fix it - do a Get Info on the alias, and also on the original of that alias. Then copy the icon from the upper left of the original's Get Info window and paste it over the wrong icon in the Get Info window for the alias. This is tedious, but need be done only once for each item. If you need additional aliases for the same item, just copy (Duplicate in Finder's File menu, or Option-drag it) the alias with the good icon.
Those icons are coming from CleanApp. If I am reading its resources in CleanApp's bundle right then it's the icon used for archives (ArchiveIcon.icns in the bundle resources). It's possible CleanApp screwed up launch services or confused the finder into associating aliases with CleanApp.
One thing you should try is to either get rid of CleanApp.app or at least compress it, say to a zip file. Bottom line, wipe that app off your system so the finder cannot see it. You may need to relaunch the finder (say, by logout and in). See if that clears your alias icon problem.