I had a problem like this recently.

I fell asleep on the couch then woke at 4am and decided to go to bed. I picked up N900 to check that the alarm was set, only to find it dead from battery depletion.

I went to bed and plugged the N900 into a 3rd party battery charger.
The N900 alarm went off on time. I tried to boot it but it showed the 5 dots then switched off. Plugging it back into the 3rd part charger showed a flashing yellow LED for a few seconds, then one blink of green, then nothing. I tried booting it a number of times with no luck. I got up, starting to feel an impending reflash coming on.

When I got downstairs, I plugged the N900 into its Nokia charger. I got a steady yellow flashing LED (which cheered me up) and went for a shower. 20 minutes later I tried to boot the N900 and it was OK (phew), it booted and showed about 50% charge.

So, from this experience, I'd suggest the following - if your N900 is playing dead, and you've been trying to charge it with a 3rd part charger, try the regular Nokia one.

Also, it is handy to know that the phone will come back from the dead to ring your alarm and get you out of bed.