Almost everything about the HD16 and MRS-1608 is similar, on the surface. Both machines feature 19 simultaneous tracks (16 audio tracks, two drum tracks and one bass) and a total of 160 tracks (16 physical times 10 virtual takes). Both have the same algorithms and effects. Both have instant mix functions and CD-burning capabilities.
The Zoom HD16 and MRS-1608 have virtual drum kits pre-programmed, but these features vary some between the two machines. The HD16 has 21 kit sounds with 27 sounds per kit and 11 bass programs. The MRS-1608 has more variety, with 50 kits each that have 36 sounds and a 13-sound bass generator.
A key distinction between the HD16 and the MRS-1608 is the hard drive capacity, which dictates the amount of recording time available. The HD16 has an 80GB hard drive, whereas the MRS-1608 only has a 40GB hard drive available. This translates to a total of about 240 hours of recording for the HD16 compared to 120 hours for the MRS-1608.
For what it's worth, the MRS-1608 is the flashier of the two, with a visual LCD equalizer and multi-colored channel selector lights on a flat machine. Its touch pad controls are blue and red, set against dark gray. The HD16 is monochromatic and a bit bulkier with a small display above the fading dials.