Codekit, Creative Suite, Evernote, Finder, Fontbook, iTunes, Reeder, Soulver, Sparrow, Quicktime. You could run photoshop.exe in Wine but there are bugs. There are alternatives to the other apps though, but they are not as polished.

Finder? Really? I would never imagine anyone would miss using Finder. That's the bit of MacOS I found hardest to get used to. Looks good, but it's completely basic and featureless, and missed the versatility of KDE's Dolphin for quite a while until I found out about TotalFinder. Despite TotalFinder being a great improvement over vanilla Finder, I still miss some of Dolphin's features such as: the ability to browse remote locations (FTP, SSH) and the ability to run a terminal window within dolphin for the folder you are viewing.

While I'd agree that overall it is lacking, Finder does support ftp/ftps.

And afp is sweet, too, if what you need is sharing between Macs.