Halo merger trees describe the hierarchical mass assembly of dark matter haloes, and are the backbone for modeling galaxy formation and evolution. Merger trees constructed using Monte Carlo algorithms based on the extended Press-Schechter (EPS) formalism are complementary to those extracted from N-body simulations, and have the advantage that they are not trammeled by limited numerical resolution and uncertainties in identifying (sub)haloes and linking them between snapshots. This paper compares multiple EPS-based merger tree algorithms to simulation results using four diagnostics: progenitor mass function (PMF), mass assembly history (MAH), merger rate per descendant halo, and the unevolved subhalo mass function (USMF). In general, algorithms based on spherical collapse yield major-merger rates that are too high by a factor of two, resulting in MAHs that are systematically offset. Assuming ellipsoidal collapse solves most of these issues, but the particular algorithm investigated here that incorporates ellipsoidal collapse dramatically overpredicts the minor-merger rate for massive haloes. The only algorithm in our comparison that yields MAHs, merger rates, and USMFs in good agreement with simulations, is that by Parkinson et al. (2008). However, this is not a true EPS-based algorithm as it draws its progenitor masses from a PMF calibrated against simulations, rather than `predicted by EPS. Finally we emphasize that the benchmarks used to test the EPS algorithms are obtained from simulations and are hampered by significant uncertainties themselves. In particular, MAHs and halo merger rates obtained from simulations by different authors reveal discrepancies that easily exceed 50 percent, even when based on the same simulation. Given this status quo, merger trees constructed using the Parkinson et al. algorithm are as accurate as those extracted from N-body simulations.
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