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I need the most secure method for syncing OF for Mac, iPhone, and iPad. That would be which choice?
  1. WebDAV on the server that hosts the company website and supports https (not local)
  2. Bonjour
  3. Time Capsule

Data being transferred may contain confidential customer information and needs to be protected from prying eyes. The mobile devices are in the office enough that at least weekly updates could happen on the LAN but remote syncing is frequently used. Privacy and security are the two big issues, besides reliability.
As for time capsule I have heard numerous reports about it being pretty unreliable in terms of product life time and hence data availability. It breaks after a short time, for many people. Plus it is a small device that everybody could easily take away, and with it your data.

Not being an IT security expert I would sync with the companies server. If it uses https then you have a chance that your data stays yours. However, depending on which branch you are in, I would recommend you invest a few bucks into an IT security specialist to set up and maintain a solution that fits your needs. It's an investment but losing customer data can easily cost you a lot more. Plus you can use it as an argument if you present yourself to new customers. Data security is a strong need for many. On the other hand I would refrain from trying to set up a secure solution on my own with the help of advices collected from multiple online forums. Without offending anybody, you never know what kind of advice you will get and if it fails then there's nobody to hold accountable for the loss.
Christian makes several excellent points - if it helps at all, option 1 offers what I personally consider to be the best mix of convenience and security in the general case. "Use the company's server" is also the option I use for my own data, but that's predicated on syncing to a box run by our specific server admin. That option needs to be evaluated on a case-by-case basis, in other words; don't just rely on a fiat recommendation.

My second choice would probably be Bonjour, but keep in mind that the closed-box nature of Bonjour means it's simple as pie when it works, and a total pain when it doesn't, with very little middle ground between the two extremes.

I don't have any experience setting up a WebDAV server on a time capsule, so I don't feel qualified to offer any opinions re: that option.

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