The research overviewed in this dissertation concerns highly accurate variational calculations of small molecular systems without assuming the Born--Oppenheimer approximation. The centerpiece of the research is the use of different forms of explicitly correlated Gaussian basis functions. These basis functions allow analytical evaluation of all necessary matrix elements and provide a very powerful tool for solving quantum mechanical problems encountered in various areas of physics. Most of the derivations presented in the dissertation are done within the formalism of matrix differential calculus that has proven to be a very handy and effective way of dealing with explicitly correlated Gaussians. As this fomalism is not widely used in physics or chemistry, some mathematical background is provided. The expressions obtained theoretically were implemented in a computer code that was run quite extensively on several parallel computer systems during the period of the author's Ph.D. study. The results of many such calculations are presented and discussed. The dissertation is primarily based on the content of the papers that were published in coathorship with my scientific advisor and other collaborators in several scientific journals. It also includes some topics that were not considered in the publications but are essential for the completeness and good understanding of the presented work.