There are a variety of ways to raise funds and communicate with your supporters online. The very basic is an online donation button. You can also host online auctions or get a commission on items sold through an online store.
Online Donation Systems
Acceptiva - Accept a variety of online donation types: contributions, tithes, school tuition payments, contributions, recurring gifts, offerings, pledges, membership fees, tickets and merchandise sales.
Active Giving - Offers a variety of services such as online donations, event management, ticket sales and membership management.
AlumniFidelity - Helps universities, schools, non-profits and individuals raise funds online. Includes personal fundraising pages.
Artez - Five modules including online giving, memorials, and event management.
BlackbaudNow - System that uses paypal to process online donations. Also offers website builder (with free hosting) and email tools.
Click & Pledge - Platform combines online donations with event management and ticket/merchandise sales.
Convio - Provides software and services to help nonprofits use the Internet strategically to build strong relationships with constituents for driving fundraising, advocacy and other forms of support.
Firstgiving - Firstgiving’s Personal Fundraising Pages are being used by organizations of all sizes for online fundraising for pledge based events.
Give Forward - System that helps any group or individual to collect donations online.
Google Checkout - A fast, convenient donation process that you can use it to process donations by charging credit or debit cards.
Kintera - Friends Asking Friends® online fundraising system allows non profit groups to collect donations for individual and team based events online. Other module include volunteer management, workplace giving and more.
Paypal - A very basic online donation processing service. Many potential donors may already have Paypal accounts setup. Plus charities get a 25% - 35% discount off the published PayPal rate.
Network for Good - This site brings together donors, volunteers and charities online. Non profits can post volunteer requests and collect donations. Individuals can search for opportunities.
Tipjoy - A simple payments solution that works well with social networking sites and blogs
Online Shopping Malls
a Good Cause - has a variety of sites tailored for different countries
Buy for Charity - Features 350 Stores with up to 35% of the order going to the shopper’s charity of choice. 
Donation Street - An online shopping mall where non-profits can earn extra money when their supporters shop online through this website. There is no cost to the non profit organization to join.
iBakeSale - Online shopping mall alternative to the bake sale
iGive.com - List over 650 online stores with up to 26% of the purchase price going toward the shoppers favorite charity.
Maatiam - Shop and support a charity. Sends donation checks quarterly.
Readerslink - Supports education based charities and schools
Visit Our Mall - Offers a wide variety of merchants with a built in follow up system. Free to join.
Other Online Fundraisers
cMarket - Easy to use online auction system for non-profit causes
eBay Giving Works - run a charity auction through eBay
Goodsearch - Earn money for your group simply by searching the internet.
Kudzu.com - Connects people with the best providers for their home, health and other life service needs. Your group earns $0.75 for each review written by you and other participants in your organization.
Online Magazine Sales - Online magazine fundraising is an easy way to raise money for a non profit organization. The magazine company processes all the orders.
Fundraising Via E-mail
Marc Pitman’s “$100,000 Guide to Email Solicitation” e-course (scroll down to the email signup form at the bottom of the page)
Fundraising on the Internet: acquiring and cultivating donors with e-mail and the Web - article by Nick Allen, published on Mal Warwick & Associates website
Using the Internet to Raise Funds and Build Donor Relationships - A free guide from Convio that covers online fundraising basics such as email list building, developing donor relationships online, creating effective online fundraising campaigns and measuring online success.
Magazine Fundraiser via Email - The online system sends out personalized emails inviting supporters to order magazines. Review
Email Management Services
Your Mailing List Provider - Reliable and affordable for small groups
Emma - offers customized email template; 20% off all fees and services for non-profits (with one year commitment)
Constant Contact Email List Manager - popular with non-profits; offers a 60 day free trial
Aweber - autoresponder & Email management system
Other
Charity Navigator - look up ratings on charities
Better Business Bureau - verify a charity, get the BBB seal of approval for your charity
Feedburner - optimizes RSS feeds