The best way to power an HDD is trhough a powered hub.
I've bought a 5V 2A power adapter (~9$) and powered both the hub and the Pi as shown in the diagram below:
5V2A ------+--- USB HUB =--- HD (USB Y-cable from HUB to HD)
(power) | | (USB from RPI to HUB)
2A is enough to power keyboard, mouse and a WiFi dongle if needed. In my case the keyboard and mouse go into the USB hub (which is a 4 ports micro hub) and the wireless dongle into the remaining USB port of the RPI.
Here are some pictures:
The connection between RPi and the hub is done with a very short (made by me) cable.
In the picture below you can see the two USB ends of the Y-Cable from the HDD.
Everything working together:
The blue light you can see at the top is the HDD Led. The Hub led is not visible in the picture.
A black plastic strip ensure there's no electrical contact between the Pi and the Hub (and also serves as SD card holder.
I will probably strip this box soon and re-assemble everyithing in a better box.
Just in case you're interested, for my other RPi (headless server used as NAS, Torrent, Backup, etc) I bought an external 2TB and reused a 12V (60W) power adapter that also has a 1A usb output (which I used to power the RPi):
The HDD USB is directly connected to the RPi USB.