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I'm not an iPhone-only user. Having used the desktop version for years before getting an iPod, I would find it crippling to only be able to use the iPod/iPhone version at the moment, as there is just too much functionality that isn't there yet, not to mention the ease of doing large-scale (re)organization of material with a keyboard on which I can rapidly touch-type, a mouse or track-pad, and several dozen times as much screen space :) I say this not to discourage you from being an iPhone-only user, just to suggest that someday you might find yourself with enough material in your database that being able to use the desktop version in addition will make life better. I find processing my Inbox to be much easier on the desktop, for example, as I can select multiple items and file them all simultaneously.

As for the Bonjour vs. WebDAV/MobileMe issue, I've used both successfully. Bonjour will get you the fastest possible syncing. You don't have to pay for it, as long as your Mac has a wireless connection, and you have a copy of the desktop application (which provides the server). It probably isn't so good for you as the only solution because you say you are away from the Mac for long stretches, and during those times you would be unable to sync (you have to be on the same wireless network as the Mac) and thus would have no backup.

With MobileMe or other WebDAV solution, you may or may not have to pay (there's a sticky on one of the OmniFocus forums talking about free WebDAV options, and I can attest that SwissDisk's free offering was easy to set up and worked well in my experiments). If you have internet connectivity, you should be able to do a sync and thus get your data backed up somewhere other than that small gadget which is so easy to misplace, have stolen, etc. Sync will probably be a bit slower, as you'll most likely be making a connection to some remote server in the cloud. OmniFocus does slow down as unsynced transactions accumulate in your database, so being able to sync at least every few days will probably make for a better experience than if you go weeks between syncs and make lots of changes to the database.

For archiving and purging, the desktop version is the clear winner. Besides the built-in archiving (which may or may not be suitable for your needs, depending on whether you need to keep some of your old completed work in the active database for reference purposes), you can manually archive stuff by simply dragging and dropping, and there is a fairly rich set of display organization tools to let you ferret out the oldest stuff so that you can delete or archive it as you please. No good way to do that on the iPhone/iPod at the moment. Arguably, the greater difficulty posed in getting a huge volume of stuff into the database with only the iPhone pays off here, as the flip side of not being able to get as much in means there isn't as much to get out :)