CJam, 18 17 bytes

0{sN1$e`2af.b}ri*

Thanks to @MartinBüttner for golfing off one byte!

Try it online in the CJam interpreter.

CJam, 18 17 bytes

0{sN1$e`2af.b}ri*

Thanks to @MartinBüttner for golfing off one byte!

Try it online in the CJam interpreter.

How it works

0                 e# Push 0.
 {           }ri* e# Repeat int(input)) times:
  s               e#   Stringify the element on top of the stack.
                       EXAMPLE: [[[1 1] '1] [[1] '0]] -> "11110"
   N              e#   Push a linefeed.
    1$            e#   Copy the last stack.
      e`          e#   Perform run-length encoding.
                  e#   EXAMPLE: "100110" -> [[1 '1] [2 '0] [2 '1] [1 '0]]
        2a        e#   Push [2].
          f.b     e#   For each pair [x 'y], execute: [x 'y][2].b
                  e#   This pushes [x2b 'y], where b is base conversion.

CJam, 18 bytes

0s{N1$e`2af.bs}ri*

Try it online in the CJam interpreter.

CJam, 18 17 bytes

0{sN1$e`2af.b}ri*

Thanks to @MartinBüttner for golfing off one byte!

Try it online in the CJam interpreter.