@Cipher: I don't know EliteHRV in detail as I use it only for data capturing. But I think the EliteHRV (at least the free version) is more or less thought for lay people.
Kubios is used in many scientific studies and is very good documented. Its used algorithms are transparent and implemented according to the Task Force of The European Society of Cardiology and The North American Society of Pacing and Electrophysiology. It has many different analyzed parameters (time and frequency domain, nonlinear).
Does Kubios analyze more parameters than EliteHRV or calculate them differently? If you compare the rMSSD, PNN50, LF, HF, etc, are they the same?