As it was mentioned in the previous part of this work (Part I)—the advanced signal processing methods are one of the quickest and the most dynamically developing scientific areas of biomedical engineering with their increasing usage in current clinical practice. In this paper, which is a Part II work—various innovative methods for the analysis of brain bioelectrical signals were presented and compared. It also describes both classical and advanced approaches for noise contamination removal such as among the others digital adaptive and non-adaptive filtering, signal decomposition methods based on blind source separation, and wavelet transform.