The 15" retina can do three (and itself) via daisychaining two Thunderbolts (or just using the two ports) and with the HDMI port. Is the 13" retina able to do this as well?
According to Apple (http://support.apple.com/kb/ht5219):
4 MacBook Pro (Retina, Mid 2012), MacBook Pro (Retina, 13-inch, Late 2012), and Mac Mini (Late 2012) computers can use an HDMI-compatible device on it's HDMI port while using one Thunderbolt display, or they can use two Thunderbolt displays.
You can drive 3 including the internal on the 13". However, you cannot run 3 external displays even if not using the internal.
source: I have one and have tested this.
The new Retina 13 is able to daisychain and drive two thunderbolt cinema displays, as explained in this very nice article:
Since the 13" MacBook Pro uses the same Intel HD Graphics 4000, DSL3510L Thunderbolt controller, and single physical Thunderbolt port as the new MacBook Air, it should be able to push a total of three monitors using daisy-chained Thunderbolt Displays.
source: Ars Technica
However, it's not clear if they can at the same time drive an extra display though the HDMI port (for a total of four including the laptop's display) like the 15 inches model can do. The 15 inches can drive 3 external and the retina display, but it has a very powerful discrete video card.
Considering that there are a lot of pixels in that configuration, I highly doubt that the integrated Intel 4000 can do it. It's a very limited video card with shared memory. But again, we'll need to find someone who can try it :)
A 13" MacBook Pro Retina late 2013 can power three external displays plus its own screen which would make four total. Here is a video showing the external displays working; 1 HDMI, 1 MiniDisplay Port, and 1 thru a USB3.0 Port using a Startech external video card to DVI adapter. All the external displays are old Apple Cinema Displays hooked up thru each monitor's Apple Display Connector (ADC), then to Apple ADC to DVI adapters, then to the relevant third adapter plugged into the MacBook. The screens are 1920 x 1200, 23 inch screens. The monitors are around 10 years old, the USB to DVI video card/adapter is around $65 Amazon.
The hardware of the 13" Macbook Pro Retina can drive three external displays simultaneously via 2x DisplayPort and 1x HDMI. The laptop display must be off, since the Intel GPU can only drive three displays simultaneously. There is a big caveat though - this is not an "Apple approved" configuration, and hence will not work under OS X. It works fine under Linux, and will probably work fine under Windows, but OS X will only allow two external displays to be active simultaneously, even with the laptop display off and the lid closed. This is true regardless of whether the DisplayPort adaptors are active or passive.
Actually it is possible using Active connectors. I ran into this issue and solved it. I've written a full article @ http://mkn.us/blog/how-to-use-3-external-monitors-on-macbook-pro-2015/
You can run 3 to 4 external monitors (4 or 5 including the main screen). This is done through USB. This video explains everything. No discrete graphics card needed, just stock macbook.