I built a loft bed when I was in college - it really helped with creating extra room in the room.
I basically had a steel frame already that clipped into drip-in "L" brackets on metal head and foot boards.
So I got 4X4's and made similar "L" brackets out of angle iron with a drill and grinder. Then I bolted these brackets to the 4X4's and put ladder braces (similar to the pics on your site) on the ends, and a big "X" brace across the back. Then my existing steel frame slipped into the new much taller head and foot boards.
Then I just used my regular desk by sliding it inderneath the bed.
Here's a link for plans that include an end desk, and bookshelf, and you can
DL for free...
http://www.bhg.com.au/home_improveme..._bunk_bed.pdf/$FILE/200104_bunk_bed.pdf