The BBC's news service, News Online, is nominated for best news service; Radio 4's website is recognised in the best radio category and BBCi is shortlisted in the best TV category.
Commercial website Amazon.com has two nominations, as does the website of magazine National Geographic.
The Webbys, as they are known, have become the most prestigious internet awards since their birth in 1996.
About 60 prizes are handed out to sites dedicated to topics as diverse as news, games, humour and spirituality.
In the news category, BBC News Online will compete with allAfrica.com, Arts and Letters Daily, Debkafile and Poynter.org.
E! Online, Who Wants to be a Millionaire?, The Osbournes and CSI are BBCi's rivals in the TV category.
Commerce
The website for Irish radio station RTE Interactive radio, Transom, Youth Radio and kpig.com are also shortlisted as best radio site.
Last year, the BBC's World Service radio website won the prize.
Amazon and National Geographic are both nominated for best practices, while Amazon is also recognised as best commerce site.
A best print and zine nomination also goes to National Geographic.
"With more than 500 million people online today, we've reached a stage where the web is part of the fabric of our lives," said Maya Draisin, the executive director of the International Academy of Digital Arts and Sciences, the organisers of the Webbys.
"The 2002 nominees - both large and small - are setting the standards for the medium and transforming the way we live."
Tiffany Shlain, founder and director of The Webby Awards, said: "The 2002 nominees demonstrate that the web is really getting back to what it does best - connecting, building communities, entertaining, and enhancing everyday life."
The nominations include:
Best education
eNature - www.enature.com
Exploratorium - www.exploratorium.org
Jason - www.jasonproject.org
MarcoPolo - marcopolo.worldcom.com
Students Against Testing - www.nomoretests.com
Best film
Donnie Darko - www.donniedarko.com
Ifilm - www.ifilm.com
Metacritic - www.metacritic.com
Waking Life - www.wakinglifemovie.com
Without a Box - www.withoutabox.com
Best music
All songs considered - www.npr.org/programs/asc
Freemuse - www.freemuse.org
Hearts of Space - www.hos.com
Live365 - www.live365.com
Looplabs - www.looplabs.com