Cloak's UI is a minimal file browser similar to Finder's "Column View" that will show you all of your files. Hidden files are shown in gray, as shown here:
Select the folder or file that you want to show/hide, and check the box next to "Invisible Finder Attribute." Voilà, the file will be hidden in Finder, although you can still access it using the Go » Go to Folder... command.
Current versions of Dropbox will sync these extended attributes, meaning that if you hide them on one computer, they will automatically be hidden on all of your Macs.
You can use Cloak for any file or folder, not just Dropbox. For example, many apps put their data in ~/Documents/ and don't give you the option to store them elsewhere, so you may want to hide some of them as well.
For the Terminally Geeky...
If you prefer the commandline, you can use SetFile -- assuming you (like any self-respecting CLI enthusiast) have the developer tools installed.
SetFile -a V foo
will set the folder/file invisible.
SetFile -a v foo
will make it visible again. You can do this to several files/folders at once, just include all of their names at the end of the command. For example, this is what I did to unclutter my Dropbox folder:
SetFile -a V Printopia Readdledocs_sandbox Thawte\ Roots/ IndexCard GoodReader Elements NoteAndShare BBEdit
Show It All
Just for the sake of completeness, I should also mention that if you want to see all of these files in the Finder, you can enter this in Terminal:
defaults write com.apple.finder AppleShowAllFiles TRUE
and when you decide that they were better off hidden, revert that command using
defaults write com.apple.finder AppleShowAllFiles FALSE
Be sure to restart Finder after each of those commands. If you want to avoid the Terminal for those commands, use the Secrets preference panel. Look for the Finder option "Show hidden files" and check or uncheck the box as desired.
Thanks to fellow TUAWers Mike Rose and Brett Terpstra for helping me track down a GUI app for setting the hidden attribute.