Update: This article on Boston.com explains the events that caused the train delays: http://www.boston.com/news/local/breaking_news/2007/11/hundreds_of_nor.html
Coming home from Cambridge after 8pm, my options are this: I can catch the 8:35pm train from North Station, or catch the 9:20pm bus from Malden Center. Both go to more or less the same distance from my house. The 8:35pm train stops at Malden, so I get off the Orange Line there and figure I'll catch the train. I get my ticket, head up the stairs, and... there's already a train there.
And it's dark.
And there's nobody on it.
And there's four people on the platform- three potential passengers and a conductor- looking confused. (Well, the conductor didn't look so much confused as just bored.)
Long story short: The train isn't going anywhere. It's inbound (and I'm outbound) and it can't leave because there's a "signalling problem" at North Station.
Fifteen minutes or so pass before the train can head in to North Station and presumably let the rest of the trains through. The train takes off. A few minutes go by. The next Orange Line train comes in.
And within a minute and a half, the empty platform is suddenly packed with angry people from Maine, including two guys in full National Park Service Ranger uniforms and an Amtrak conductor. Not an MBTA/MBCR conductor, but Amtrak. And she loudly announces that she doesn't know anything yet. "I don't have any information yet! I will let you know when I do!"
Incidentally, the MBTA apparently didn't know either-- the T station attendant at Malden came up when the commuter rail train was there because a passenger had asked her what was going on. Nobody had told her that there was a train stopped at the station, she told me.
Near as I could gather from everyone, there was either a derailment or the potential for a derailment at North Station as the Downeaster, which is Amtrak's only passenger service out of North Station, was about to pull out. And all trains on that line were then screwed, which is why the inbound commuter rail train had been sitting darkened when I arrived at Malden. The Downeaster does not usually stop at Malden Center as near as I can tell from the Amtrak site. And I'm reasonably sure it doesn't use the Boston-Reading part of the line in normal operation but takes the alternate Boston-Woburn-Haverhill route.
Somebody at North Station had all of these people get off the Downeaster and take the subway to Malden Center so that they could get back on the Downeaster. I heard one guy complaining, "We were on a warm train! With a bar!"
Finally the Amtrak conductor got on a bench and announced to everyone that she had finally been given some information-- "Both the Downeaster and the commuter rail train are getting ready to leave North Station. If you are going to Haverhill or are a Downeaster passenger, get on the Downeaster. If you are going anywhere between here and Haverhill, you have to get on the commuter rail. I do not know which one is getting here first."
Naturally, the first question somebody asked her after her announcement was "Which one is getting here first?" She was remarkably restrained. =)
The Downeaster came in first, by which time the bus was about to be leaving Malden Center and I took that instead.
Why the Orange Line isn't just extended to Melrose and Wakefield is beyond me. I've heard that the problem is that Melrose blocked it from happening but I can't find anything definitive on that.
I also wonder if the Downeaster passengers had to pay to get on the subway from North Station to Malden. Or if they'll get refunds for the inconvenience they experienced.

