Dear ZlatkoMM, the varactors based on NPN transistor have usually low Q when the C-B junction is used (due to high series resistance). On the other hand, this junction has usually high Miller capacitance, what is desirable for varactor operation. Therefore, the C-B junction capacitance change is suitable for short or medium-wave oscillators (several MHz). The B-E junction has lower series resistance, and therefore you can experience higher Q than the above mentioned counterpart. On the other hand, the width of base area is small and the emmitter is highly-doped, so the breakdown voltage of this junction is very low (usually about 5V) and such varactor is quite noisy near Vbr.