I suspect the best choice as far as a good yield would still be ethanol precipitation. If it is ok, you can add a final concentration of 10 mM MgCl2 during ethanol precipitation to help DNA aggregation. Very small amounts of DNA can be recovered efficiently. Also, I would suggest leaving the DNA solution at -20C overnight (rather than shorter incubations) and perhaps spin extensively (40-45 min) during recovery. However, if you use your DNA for transformation by electroporation, the Mg ions may give you some problems. Good luck.

You may use a kit such as (http://vivantechnologies.com/index.php?option=com_content&view=article&id=73:gf-1-nucleic-acid-extraction-kits&catid=12:news&Itemid=7) to chance buffer. It capacity to bind low molecular weight DNA? Just check them... Good Luck

Ethanol precipitation with 2 mM Mg(OAc)2 probably should work. If not, you will need to bind the DNA to DEAE or Qiagen.

Add water to 200μλ and then add 2.5 volumes of Et-OH and 1/20 to 1/10 volume of CH3COONa 3M ph 5.2 (the pH should be adjusted with CH3COOH) leave your sample O/N in -20C or in -80C for 45 min (I prefer O/N). Centrifuge your samples for 20min at 4C in 13.000 to 15.000 rpm. Get rid of the supernatant. Dilute the precipitate in 300μλ of 70% Et-OH. Centrifuge again at room temperature in maximum speed for 20 min. Get rid of the Et-OH. Leave your tube to dry and resuspend your DNA in your favourite buffer. I hope that be helpful.

Thank you all. It seems that almost everybody suggests precipitation: I will try to add MgCl2 and will post feedback here! @Ted I aleady tried to speedvac, but the pellet was too much gelatinous and I could not even use it for gel electrophoresis

For small fragments of DNA Ethanol precipitation in presence of glycogen works very good. it helps to precipitate creating a matrix and it does not affects further reactions as electroporation or restriction enzyme manipulation. You can find it in some molecular biology catalogs