Data and metadata from my PhD research on the effects of non-native grass litter in coastal sage scrub communities are freely-available though the Knowledge Network for Biodiversity (KNB). GPS locations for plots are available upon request with approval from the field site's biologist.
Data for my phenology review paper with Steph Pau are freely-available through KNB.
The NCEAS 'Forecasting Phenology' working group that I led with Ben Cook created the STONE (Synthesis of Timings Observed in iNcrease Experiments) and NECTAR (Network of Ecological and Climatological Timings Across Systems) databases.
USA National Phenology Network maintains a good list of historical phenology datasets here.
Fitter & Fitter's dataset of first flowering dates in Chinnor, England is available with their Science article.
NOAA maintains a short list of several phenology datasets here.
Much of Europe's phenology data (especially the International Phenology Gardens) were organized through their COST 725 action, which morphed into PEP725. See also PPODB, a database focused on Central Europe and its related article here.
The KNMI Climate Explorer site maintains a great set of organized resources.
Plant trait data:
USDA PLANTS is a stand-by for US work, the TRY initiative has combined a large database of plant functional traits and is working on using cutting-edge bioinformatics techniques with it. Also based in Europe is LEDA. For the British Isles Ecoflora is fantastic. Also, the Angiosperm Phylogeny Website has useful info, as does Watson and Dallwitz's Families of Flowering Plants.
I indentified ants to species with help from the tremendous resources available at Antweb.
Harvard's MCZ museum has a good database with layered images of Caribbean insects.