We have been storing integrated transformants in large numbers with
good success in 96 well plates. We innoculate 150 microliters of YEPD with cells and leave them for two days at 30 degrees to grow. Then we add half a volume
of 50% glycerol (so less than 25%), stir with a pipet tip or toothpick and
store at -80 degrees. The cells can be recovered by scraping a toothpick over
the frozen culture (I haven't tried one of those multichannel pipettors to do
a whole row at once, but I will probably eventually).