An overview is provided of the present population analysis methods and an assessment of which software packages are most appropriate for various PK/PD modeling problems. Four PK/PD example problems were solved using the programs NONMEM VI beta version, PDx-MCPEM, S-ADAPT, MONOLIX, and WinBUGS, informally assessed for reasonable accuracy and stability in analyzing these problems. Also, for each program we describe their general interface, ease of use, and abilities. We conclude with discussing which algorithms and software are most suitable for which types of PK/PD problems. NONMEM FO method is accurate and fast with 2-compartment models, if intra-individual and interindividual variances are small. The NONMEM FOCE method is slower than FO, but gives accurate population values regardless of size of intra- and interindividual errors. However, if data are very sparse, the NONMEM FOCE method can lead to inaccurate values, while the Laplace method can provide more accurate results. The exact EM methods (performed using S-ADAPT, PDx-MCPEM, and MONOLIX) have greater stability in analyzing complex PK/PD models, and can provide accurate results with sparse or rich data. MCPEM methods perform more slowly than NONMEM FOCE for simple models, but perform more quickly and stably than NONMEM FOCE for complex models. WinBUGS provides accurate assessments of the population parameters, standard errors and 95% confidence intervals for all examples. Like the MCPEM methods, WinBUGS's efficiency increases relative to NONMEM when solving the complex PK/PD models.