I think we need to know what it is you're trying to achieve; what do you mean by "highest level of security"?  How securely programmed the email app is coded?  Confidentiality/integrity of the local mail store (PST, etc)?  The security of the transmission of the emails from the email app to the server?

MaXe touched on secure programming of each app a bit.  ajohnson touched on securing the local mail store by encrypting it.  Maybe you're referring to the transmission of email?

During the setup of a web app to connect to web-based mailboxes (speaking from experience configuring Outlook/Thunderbird to connect to a Gmail mailbox), you configure encryption types (SSL/TLS) when sending/receiving mail from the email app to the mail server (Gmail in this case).  I haven't used Outlook and Exchange in awhile, but I believe there's security built into the protocol used by Microsoft to transmit mail between the client's mail app and the Exchange mailbox.

I believe you'll be using IMAP/SMTP for email transport when using any email app other than Outlook (when using Outlook with Exchange, Microsoft has their own transport protocol) and this depends on the configurations of the mail server more than anything.  I think most email apps allow you to select none/SSL/TLS for encryption options for IMAP/SMTP along with the ports to use, it just depends on what the email server is configured for.