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Thanks for the quick reply.<br />
<br />
When you say that guest links are not available for folders, does that mean people outside of your own Office 365 tenant are treated as guests or if they are signed in to their own tenant, they are not guests, but signed-in users of their own tenant?<br />
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The reason I'm asking is because it's not going to work if we can't provide access to folders for other users in other companies.
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you can grant access to parts of your environment to Microsoft account / MOSS users.<br />
use the usual sharing options in SharePoint online and grant permission to them.<br />
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Microsoft appear to have exited the 'public website' features of SharePoint online.<br />
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Azure AD is your friend
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Guest links = anonymous access, if they are signed as another O365 user (in external company), they dont count as guests and you can share folders.
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We have Office365 and are very new to SharePoint. We know you can use SharePoint as a repository to store and share files but not entirely sure the best way to do this. <br />
<br />
Documents will be shared with users in the same company as well as users in other companies. Users will need to be able to read and edit folders and documents on a case-by-case basis.<br />
<br />
Is SharePoint the best way to do this or would it be easier to organise just using OneDrive?
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We have Office365 and are very new to SharePoint. We know you can use SharePoint as a repository to store and share files but not entirely sure the best way to do this. 

Documents will be shared with users in the same company as well as users in other companies. Users will need to be able to read and edit folders and documents on a case-by-case basis.

Is SharePoint the best way to do this or would it be easier to organise just using OneDrive?

Sharing Files Externally in SharePoint

Microsoft Sharepoint is a software platform and family of software products used for collaboration and web publishing combined. These capabilities include developing web sites, portals, intranets, content management systems, search engines, wikis, blogs, and other tools for business intelligence and collaboration. SharePoint has a Microsoft Office-like interface, and it is closely integrated with the Office suite.

Microsoft SharePoint

Office 365 is a group of software plus services subscriptions that provides productivity software and related services to its subscribers. Office 365 allows the use of Microsoft Office apps on Windows and OS X, provides storage space on Microsoft's cloud storage service OneDrive, and grants 60 Skype minutes per month. Office 365 includes e-mail and social networking services through hosted versions of Exchange Server, Skype for Business Server, SharePoint and Office Online, integration with Yammer, as well as access to the Office software. All of Office 365's components can be managed and configured through an online portal; users can be added manually, imported from a CSV file, or Office 365 can be set up for single sign-on with a local Active Directory using Active Directory Federation Services.