Ok, I'm going to give a fully unbiased summary of what I have collected over my interest of photography, and hopefully, even Nemesis won't disagree(we always get in debates over photography for some reason).
You want autofocus is is a good feature to have. And it can be turned off if you want, so drop the idea of "no autofocus capability > the option to have AF."
The Nikon D40, D40X, andD60 all lack the in-body focus motor, and this means you cannot use older Nikon lenses with the feature of autofocus. You can still focus manually, but it's much slower, and can be reletively hard to get right through the tiny D40 and other entry level viewfinders(especially if you've used a full frame film camera's viewfinder). For those aforementioned Nikons, you have to buy AF-S lenses, with an in-lens autofocus motor, rather than a body driven focus. Is this bad? Well, not if you're buying new Nikon lenses, but if you're scrounging around for old film lenses on Ebay to save money, they may not AF. If you go the Nikon route, Get an older D50, D70, or D70s with some nicer old lenses, for the budget route. If you don't mind saving the money on a brand new body, but risk more expensive lenses, go for a newer D40, D40X, or D60. If you want the best of both worlds, try and get a D80(or D90 might be out, I haven't followed up on it).
If you go the Canon route, you can use all EF mount lenses back to 1987, my cheap ass has 2 EF lenses BOTH with 1987 time stamps on the mount. Each lens cost me roughly $80. They're older, and autofocus a tad bit slower than their newer counterparts, but they perform like $350 lenses (about middle class lenses by today's standards).
Sony lets you use the Minolta line of lenses, which are nice and cheap, but Sony seems to have control issues with developing their OWN media (Memory Sticks, Blu Ray, a special hot shoe for flashes, etc. etc.) and they might keep switching things up for a little while.
Pentax cameras are really full featured, and the newest models are made in a way to accept all Pentax lenses made in the past 50 years, through adapters. Some features may not make it into translation on the body, such as obviously not having autofocus on a 30 year old lens, but the oldies can be cheaper than dirt.
Olympus cameras I'm not too knowledgeable on, so I'd rather not say something false.
I don't know if I missed any but I hope all this helps. Pretty much any brand will yield you the same results, they each have their pros and cons.
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