Samsung has kept using Super AMOLED panels for its top of the lines products, but that may change this year, as some of their devices, especially the Note series may be switching to LCD for better experience with the active digitizer and the S-pen.
Perhaps there's a technical reason why the S-pen works better with LCD than AMOLED, or perhaps its because people want more accurate colors for drawing stuff, and Super AMOLED doesn't really provide that, or it could just be because the S-pen adds enough to the cost of the device, even without the Super AMOLED display. Super AMOLED displays tend to be significantly more expensive than their LCD counter-parts, when at the same resolution (that's why you usually see Super AMOLED devices arrive with lower resolution than the IPS LCD's ones in other products – like in the Note 2 for example).
Samsung has recently invested in Sharp's display division, and according to insiders, Samsung thinks Sharp makes the best LCD displays on the market right now. Both Sharp and Samsung make displays for Apple's own iOS devices, too. This doesn't necessarily mean Samsung will stop using OLED-type displays altogether, though. The Galaxy S4 is rumored to have a "PHOLED" display, and there's still the YOUM flexible display, which I'm sure it will be used and promoted greatly by Samsung, because it's one thing they have and their competitors do not.
But it does look that for whatever reason they will be using LCD with the S-Pen on the Galaxy Note devices like Galaxy Note 8.0, Note 3, and the next-gen Galaxy Note 10.1. This should also ease up the panel supply from their own division, as Samsung is a big enough company that they can't even depend on themselves alone to supply all the panels for all the devices they are making. that's why they also tend to use chips from other chips makers, too, such as Qualcomm or Nvidia.
Also, these days I tend to prefer IPS LCD anyway because of its more accurate colors. Perhaps Samsung should consider moving almost completely to IPS LCD's, with the exception of YOUM panels.