Nomenclature of compounds by the IUPAC
Certainly, the most important organization for chemical nomenclature is the International Union of Pure and Applied Chemistry (IUPAC). In most cases, the various IUPAC recommendations represent the best references.

However, not all IUPAC recommendations are universally accepted. For example: 


The correct internationally standardized name of element 111 is ‘röntgenium’; IUPAC recommendations spell it ‘roentgenium’, which is explicitly considered wrong by international standards.  
According to current IUPAC recommendations, the formula of ions like sulfate is written as $\mathrm{SO_4{}^{2-}}$, which has not yet gained much acceptance. According to ISO and various national standards, the correct internationally standardized notation is $\mathrm{SO_4^{2-}}$.
In the 1970 IUPAC recommendations, a chelating ligand with two coordinating atoms was indicated by the term ‘bidentate’. In the 1990 IUPAC recommendations, the term ‘didentate’ was used rather than ‘bidentate’, for reasons of linguistic consistency. However, the term ‘bidentate’ remained in common usage, which is reflected by the reversion to the previously accepted term ‘bidentate’ in the 2005 IUPAC recommendations.
The @ notation for “fullerenes with metals inside” was proposed in J. Phys. Chem. 1991, 95 (20), 7564–7568 and became generally accepted. The corresponding IUPAC proposal, which was presented in Pure Appl. Chem. 1997, 69 (7), 1411–1434, did not use the @ symbol, but it was not as successful as the first one.


Many compounds can have two or more systematic names in accordance with several methods recommended by IUPAC. In addition, various traditional names, which have been coined and used over the years, are retained for use in IUPAC nomenclature. Therefore, current IUPAC recommendations include the definition of a preferred IUPAC name (PIN), which is the name preferred among two or more names generated from two or more IUPAC recommendations including the many retained names. Nevertheless, other names that are generated in accordance with IUPAC recommendations may be used in general nomenclature.

Apart from the large and universally active IUPAC, further smaller and specialized organizations exists, for example the International Union of Biochemistry and Molecular Biology (IUBMB). Such organizations may issue their own recommendations concerning their field of expertise. However, many of these recommendations are actually harmonized with IUPAC recommendations.

Another large and universally active organization that prescribes independent naming rules is the Chemical Abstracts Service (CAS). CAS names may differ from IUPAC names. For example, the preferred IUPAC name of Buckminsterfullerene is (C60-Ih)[5,6]fullerene, whereas the corresponding CAS name is [5,6]fullerene-C60-Ih.