I wonder if there is an opportunity with GMOs to aid automated plant identification. For instance, insert a green fluorescent protein gene in your crop, and design a robot that senses the fluorescence.
Multispectral imaging can identify weeds and separate different types of plants.[1] Humans have only 3 color sensors, but there's no reason you can't have far more. Some birds have 21. It's easy and cheap to do, although you need a camera with a special per-pixel filter instead of the usual RGB filter.
[1] http://www.bioone.org/doi/abs/10.1614/WT-07-104.1?journalCod...