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Run summary data
Run summary data log_20150116191009.txt
Taxonomy assignments
OTU taxonomic assignments rep_set_tax_assignments.txt
OTU tables
OTU table exluding OTUs with fewer than 2 sequences otu_table_mc2.biom
OTU table exluding OTUs with fewer than 2 sequences and including OTU taxonomy assignments otu_table_mc2_w_tax.biom
OTU table exluding OTUs with fewer than 2 sequences and sequences that fail to align with PyNAST and including OTU taxonomy assignments otu_table_mc2_w_tax_no_pynast_failures.biom
Trees
OTU phylogenetic tree rep_set.tre
OTU maps
Final map of OTU identifier to sequence identifers excluding OTUs with fewer than 2 sequences final_otu_map_mc2.txt
Sequences
OTU representative sequences rep_set.fna
New reference sequences (i.e., OTU representative sequences plus input reference sequences) new_refseqs.fna

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See the QIIME tutorials for examples of additional analyses that can be run.
You can find documentation of the QIIME scripts in the QIIME script index.