There are some more, usually specific ones:

Nation-wide sequencing:

Sequence variants from whole genome sequencing a large group of Icelanders, 2636 people so far

http://www.nature.com/articles/sdata201511

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data., DDBJ - DNA DATA BANK of JAPAN

http://www.ncbi.nlm.nih.gov/pubmed/23657089

Exome Sequencing: Current and Future Perspectives, many eukarytes - from humans to simplier organisms, etc

http://www.g3journal.org/content/5/8/1543.full

Plant genomes, so far - 49

https://dl.sciencesocieties.org/publications/tpg/articles/6/2/plantgenome2013.03.0001in

Some separate important human genes:

Phase-defined complete sequencing of the HLA genes by next-generation sequencing. Human leicocyte antigen

"The human leukocyte antigen (HLA) region, the 3.8-Mb segment of the human genome at 6p21, has been associated with more than 100 different diseases, mostly autoimmune diseases. Due to the complex nature of HLA genes, there are difficulties in elucidating complete HLA gene sequences especially HLA gene haplotype structures by the conventional sequencing method."

http://www.ncbi.nlm.nih.gov/pubmed/23714642

List of different projects: European Genome-phenome Archive

https://www.ebi.ac.uk/ega/datasets

And bacteria, but they are prokaryotes...