The VSL2 predictor of intrinsically disordered protein regions developed by the ISTZORAN group has been rated as the best model at the 7th Critical Assessments of Structure Prediction experiments meeting (CASP 7). An older version of this model was the best model at CASP6.
You can try the VSL2 predictor or download the VSL2 predictor package and set it up on your own machine (detailed instructions). You can choose whether to use computationally demanding features derived from PSI-BLAST profiles and/or secondary structure predictions.
Citation: Peng K., Radivojac P., Vucetic S., Dunker A.K., and Obradovic Z., Length-Dependent Prediction of Protein Intrinsic Disorder, BMC Bioinformatics 7:208, 2006.