Comfortable low end saddle and plain stem, problem solved.

No one is going to spend even 5 minutes to rip off a $40 setup.

And I hate to break it to you, but it's not just crack/methheads who steal bikes and bike parts. It's also other riders who don't have the money but still want a Thompson stem and a Brooks saddle. I've seen more than a few bike thieves busted on the USC campus and it's usually kids on fixies of their own.

Everyone's always talking about the sophistication of the bike thieves, imagining that they carry dremel tools, bolt cutters, nitro, and acetone. When in reality there are enough people who do a poor job of locking their bikes all you need to do is undo a quick release or carry a 15mm wrench. I lock up every day in downtown Los Angeles and use two Kryptonite U-Locks, no super glue, no wax in the bolt heads, and my bike is always exactly as I left it. And I don't worry about it either, because there are, on any given day a couple of way nicer bikes next to mine locked with tumbler locked cable locks. And these are the morons who then come on these forums and talk about the super-powered bike thief. They might as well just hang a "Free Bike" sign on them after they lock up. IMO the secret is just to make your bike the least desirable and most difficult target.