UK-based researchers tested the three leading desktop sequencers. The results: if you want the most throughout per hour, the Ion Torrent PGM does that. If you need the highest throughput per run, the MiSeq is there. Accuracy-wise, the MiSeq is best; for generating the longest reads, the 454 is best.

Ref.: Nicholas J Loman et al., Performance comparison of benchtop high-throughput sequencing platforms, Nature Biotechnology, 2012 [DOI: 10.1038/nbt.2198]