What is the basic difference between a standard and alternate waveform fit and when would you normally choose one over the other?

The standard waveform fit is optimized for "ice sheet-like" returns. The majority of these are single-peaked, narrow waveforms. The standard fit allows for only two peaks. Alternate waveform fitting is meant to capture up to six peaks. More peaks are necessary for more complex waveforms over land, vegetated surfaces and crevassed parts of ice sheets and glaciers. Another key difference between standard and alternate fit concerns the noise floor threshold. Initially, the alternate fitting algorithm used a lower threshold, meant to capture lower-energy peaks than the standard ice sheet waveform. Starting with Laser 2D the thresholds were set lower to account for weaker laser power, resulting in the alternate and standard fits having more similar signal area. Specifically, starting with L2D the standard fit was adjusted from 15 to 9.5, and starting with L2E the alternate fit was adjusted from 3.5 to 7.5. See also: GLAS Altimetry HDF5 Product Usage Guidance