We do them!. We're set in a wonderful part of Austria, and some of the singletrack is just in-accessable unless multi day routes are chosen. Normally a two day trip will involve a whole bunch of climbing on day one, stay in an alpine hut overnight and then an almost pedal free day home again. Longer trips vary, but we can taylor them to suit.
I have also ridden most of the GR5 from Geneva to Nice. its a great route, but pretty busy with walkers in places, and I didnt enjoy having to carry all my camping gear.
Whatever you choose, make sure you get plenty of fitness in before hand as it will make it so much more worthwhile.
Enjoy!