NetSuite, Larry Ellison’s other company, the on-demand one usually seen as a foil for Salesforce.com and its CEO, ex-Ellison lieutenant Marc Benioff, has started directing its attention to Larry’s great hereditary enemy, SAP.

It’s got a new migration program called Business ByNetSuite – a name obviously inspired by SAP’s own bollixed contribution to cloudware, Business ByDesign.

The SaaS start-up is offering SAP R/3 customers “at least” a 50% discount off their annual maintenance and support agreements with SAP if they switch to an annual NetSuite subscription.

SAP recently moved its users to an enterprise support scheme that costs 22% of their license fees, up close to 30% and described by NetSuite as perhaps “the highest maintenance fees ever levied by a major vendor in the enterprise software market.”

NetSuite’s stock in trade has been American SMEs, not a particularly promising field right now given credit crisis-engendered slow bookings, especially with ERP, which as Credit Suisse points out, is “directly impacted by macroeconomic conditions.”

Certainly that’s the way it looks judging from NetSuite Q3 results: a wider loss of $6.2 million, or 10 cents a share – up from $1.8 million last year – on revenues of $40.4 million, up 44% year-over-year and heavily dependent on the US with lower-than-expected deferred revenue growth and free cash flow and a below-average operating margin.

So going after large and mid-market SAP customers offering to cut ERP costs at the subsidiary, divisional and departmental level sounds sensible.

The company quotes the case of Asahi Kasei Fibers, which was spending 3% of revenue on SAP and is now only spending 0.1% on NetSuite – and let 13 consultants go.

With third-party software, data can be moved out of SAP and into NetSuite, or integrated with NetSuite.