Newer developments of estimation methods have shown that the quality of the Joback method is limited. The original authors already stated themselves in the original article abstract: "High accuracy is not claimed, but the proposed methods are often as or more accurate than techniques in common use today."  
The list of groups does not cover many common molecules sufficiently. Especially aromatic compounds are not differentiated from normal ring-containing components. This is a severe problem because aromatic and aliphatic components differ strongly.
The data base Joback and Reid used for obtaining the group parameters was rather small and covered only a limited number of different molecules. The best coverage has been achieved for normal boiling points (438 components), and the worst for heats of fusion (155 components). Current developments that can use data banks, like the Dortmund Data Bank or the DIPPR data base, have a much broader coverage.
The formula used for the prediction of the normal boiling point shows another problem. Joback assumed a constant contribution of added groups in homologous series like the alkanes. This doesn't describe the real behavior of the normal boiling points correctly. Instead of the constant contribution, a decrease of the contribution with increasing number of groups must be applied. The chosen formula of the Joback method leads to high deviations for large and small molecules and an acceptable good estimation only for mid-sized components.