You could hack something together using rsync, or unison. But, frankly, if neither of these things does what you want out of the box you will quickly find yourself spending more time than it's worth to save the $99 annual cost of a 50GB Dropbox account.
I use unison to sync a bunch of folders between my laptop and desktop, but only on an ad hoc basis. For stuff that I want synced in the background I use Dropbox. And, frankly, I'm not sure why I'm not using Dropbox for everything. For example, I'm running Jungledisk to make backups of my current project folders to S3 in the event of a big fire in my building... but if I just put my Jungledisk stuff in a Dropbox I believe I'd be syncing it and backing it up with versioning, all automatically. I need to look into that.
As for the clients that require verified encryption... is it possible to make an encrypted volume, created with something like Truecrype, and stick that in Dropbox? I've done that. Not sure how the task of automating the mounting and dismounting would go, nor of how secure this really is.
I use unison to sync a bunch of folders between my laptop and desktop, but only on an ad hoc basis. For stuff that I want synced in the background I use Dropbox. And, frankly, I'm not sure why I'm not using Dropbox for everything. For example, I'm running Jungledisk to make backups of my current project folders to S3 in the event of a big fire in my building... but if I just put my Jungledisk stuff in a Dropbox I believe I'd be syncing it and backing it up with versioning, all automatically. I need to look into that.
As for the clients that require verified encryption... is it possible to make an encrypted volume, created with something like Truecrype, and stick that in Dropbox? I've done that. Not sure how the task of automating the mounting and dismounting would go, nor of how secure this really is.