I'm curious whether anyone has performed parallel phage display assays using magnetic and agarose beads to compare nonspecific binding. Any sense for which produces lower background binding?
I didnt do this comparison. My only experience is directly comparing magnetic beads-based selection with panning on a plastic well surface. There was much less background in the former. But despite the differences in background, specific phage selection was able to overcome background in both cases and I got mixtures highly enriched in positive phages. So my advice would be dont worry too much about background, if there are good binders they will be retrieved.
It also depends on your "throughput level". If you are working with one antigen/one selection at a time "old school" immune tube or plastic wells can be OK, although the washing part is soul draining, specially if you increase the stringency during the selection. Magnetic beads definitely allow for automation and less hands-on approaches.