Generate the Temple Skyline Sequence

CJam, 25 23 22 bytes

ri1e>2be`z($W%a\+ze~2b

Just a bit of run-length encoding. -1 thanks to @MartinBüttner.

Try it online / Test suite.

Explanation

ri        Read n from input as int
1e>       Take max with 1 (special case for n = 0)
2b        Convert n to binary
e`        Run length encode
z         Zip, giving a pair [<counts> <10101.. array>]
($W%      Drop the counts array and sort decending
a\+z      Add it back to the 10101.. array and re-zip
e~        Run length decode
2b        Convert from binary

Pyth - 21 20 bytes

Thanks to @sok for saving me one byte!

is.em%hk2hb_Sr.BQ8 2

Try it here online.

Python 2, 121 bytes 125

121: Thanks to Sp3000 for shaving off 4 bytes!

import re;print int("".join(n*`~i%2`for i,n in enumerate(sorted(map(len,re.split('(1*|0+)',bin(input())[2:])))[::-1])),2)

125

import re;print int("".join("10"[i%2]*n for i,n in enumerate(sorted(map(len,re.split('(1*|0+)',bin(input())[2:])))[::-1])),2)