There are a number of reasons why your emails may be detected as Spam.
1) The people you are sending the email to may have strong spam filter settings on their email account, or accidentally marked a previous email from you as spam.
2) Your email Port settings may be need to be updated or adjusted, especially if you are currently using Port 25 for outgoing mail. Port 25 is a known Port for spam activity - if possible, a change to Port 443 should fix this issue.
3) The content of the emails may be flagged as suspicious due to the title of the email (e.g. obscure characters or title). Too many links in an email may also cause it to be flagged as spam.
4) We've recently introduced the ability to see, within Base, if someone has opened an email that was sent through your Base account. We do this by embedding a small tracking pixel in emails sent through Base. Though very rare, this could cause an email to be marked as spam as well.
A number of spam filters, for Gmail/Google Apps and Yahoo in particular, use content filtering to identify potential spam messages. Google's Bulk Email Guide offers some help on how to structure your emails to minimize the chance of them being flagged.