Can you recommend 2-3 CRM applications that are solid towards Indirect/Partner Sales Management?
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Salesforce has the most partner integration from my experience. SugarCRM and ZohoCRM probably has a comparable features and functionality and are lower cost.
Ultimately, Salesforce is setup to handle the partner/channel management through specific roles and views.
Any "platform" CRM that allows for unique roles and multiple association will support indirect sales. Our team uses SugarCRM because we like the power of the customization and ability to really personalize each user's experience. There are lots of great options in the Google Ap's marketplace (like Zoho). A google search of CRM will give you thousands of sites that evaluate, review, and recommend.
A platform CRM is one that is vertical neutral. There are also a host of CRM's that are specific to a vertical. Many of them will support indirect sales as well and if you find a cost effective solution that matches your space it may save you a lot of time in customization, as well as allow you to incorporate the best-of-class business processes that are built in.