I currently use Marketo and evaluated both very heavily before making the decision. Both systems have very similar functionality in terms of landing pages, email marketing, reporting, etc. The primary difference is that Marketo can act as it's own CRM system if you do not have one. Eloqua does not - which was the decision maker for us. I wanted to keep unqualified prospects separate from sales-ready prospects and customers. Marketo allows me to contain them within their solution and then pass them along once they reach a qualified state.
They both sync natively with SalesForce and other CRM solutions - Marketo was actually developed on the salesforce.com platform so it's syncing and native ability to control CRM tasks and assignment rules was stronger in my opinion.
Eloqua Corp. is a marketing automation SaaS company which develops automated marketing and demand generation software and services for business-to-business marketers. The company has been described as a pioneer and industry leader in lead generation services. Their customers are eBay, Apple, etc.
They have over 1100 clients but look who the clients are:)
Marketo is a Leader in Lead-to-Revenue Management for Large Enterprises and recognized as having the highest score in “Current Offering” for Small Marketing Teams. They had the highest scores of any vendor in the following areas:
Campaign design, execution, management
Sales tools and interaction
Reporting, analytics, and alerting
Technology and architecture
Marketo and Eloqua are the two dominant players in B2B marketing automation in terms of market share and in terms of product functionality. To learn about the differences between Marketo and Eloqua, Sam Boush, the founder of Lead Lizard, spoke with four of the smartest people in marketing automation: http://www.leadlizard.com/marketo-vs-eloqua/.