Show hidden files on OS X except .DS_Store

"You can show hidden files in Finder with a simple Terminal command:

defaults write com.apple.finder AppleShowAllFiles -bool YES

Then relaunch Finder by holding down the option key and right-clicking its dock icon.

However, you can't hide the .DS_Store files without hiding the rest of the hidden files. You probably just have to live one way or the other."

"You can't hide it, but you can make it transparent, then drag it to the bottom-left or bottom right corner. So only you will see a string "".DS_Store"", and there will be no icon.

Expert method:
Copy a transparent image from your favorite img editor, select the icon of the file in the file info window, and paste the transparent image when the original icon is selected on the top.

Step-By-Step method (Previous to Yosemite):

Find a pure-white area in a folder, then press Shift-Command-Control-4, and drag out a square. Release the mouse when done, and the white area is now on your clipboard.
Open Preview and press Command-V.
Click and hold on the Select button in Preview's toolbar, and Instant Alpha from the drop-down menu.
Click and drag across the white area until you see the displayed value reach 100%, then press Return.
Copy the selected area (Command-C).
On the desktop, select your new folder and press Command-I (File » Get Info).
(Press Tab once in the Get Info window to) highlight the default icon.
Paste the transparent icon from your clipboard into the default icon (Command-V).

Per @mliqu: In OS X Yosemite (10.10.1):

Press Shift-Command-Control-4, and drag out a square over any area. Release the mouse when done, and the area is now on your clipboard.
Open Preview and press Command-N to open a window with your capture.
Press Command-A to select all, then press Delete.
Press Command-C to copy this empty grey square to clipboard.
Select "".DS_Store"" and Command-I to get info.
Select the icon in the top-left and Command-V to replace with transparency from clipboard."

"There is this open source magic tool: asepsis. Sources are available on Github.

Version 1.4 now works with OS X Mavericks.

Update: Reported not working on El Capitan

Warning: Asepsis is no longer under active development and supported under OS X 10.11 (El Capitan) and later."