Well, among those three, the D100 is the only one that is built to last. It was the entry level "pro" Nikon when it was introduced ... but that was at least 6 years ago. So the technology is pretty antiquated.
Back then the D100 sold for $1995.00!
So, from the standpoint of quality construction and durability, it's head and shoulders better than either of the other two. But it's not nearly as sophisticated as the other two technologically. Things just change so fast these days that even the cheapest DSLRs now have more sophisticated (and in most cases, superior) sensors and processors.
I've used a D100 professionally for five years now. It's still my favorite workhorse camera. I'm upgrading soon to a D300, but I'll keep the 100 around as a backup.
For around $600, you'll be getting a Used - maybe VERY used - D100. So I'd be real careful there. And if someone is selling you a "brand new" D100, just be aware: Nikon quit making them a LONG time ago, so it's probably been sitting forgotten on a shelf somewhere for quite a while.
The D40 and the Rebel are very lightweight, plastic camera bodies. They're not designed to last more than a couple of years. So don't expect them to. They're strictly entry level DSLRs. But add some decent lenses and a good flash, and then when the camera body dies just replace it.