I want to be able, in some quantitative way, to compare several plant species with respect to how much is known about the functions of all known loci in their genomes.
It seems like looking at the tags for each locus in different functional annotation or protein databases (i.e. Pfam, PANTHER, KOG, GO BP) might just be reflective of the species' evolutionary relationship to Arabidopsis, for which most of what we know about plant protein function has been determined. Are there any publicly available datasets that I could use to approximate the sum of all functional work done in each plant that would be comparable across species? How could I analyze them to roughly answer the question: "what proportion of the genome has been functionally characterized?"
A plant version of ENCODE project does not seem to exist yet. But the Plant Chromatin State Database may be useful toward your goal:
http://systemsbiology.cau.edu.cn/chromstates/
You can do a rough estimation based on how many genes which are inventoried in a specifically sequenced genome, ratio it over the theoretic gene number over such species or related species. You can even use estimated human gene number as guidance for estimation according to their function complexities. The real question is how many genes a species really have.
This paper may be helpful to you.
Article Open questions: How many genes do we have?
Use arabidopsis gene number (27,655) as a lower boundary of plant gene number estimation related to the species you're interested, because of low repetitive DNA content in arabidopsis genome.
https://www.arabidopsis.org/
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