I bought this game today and installed it. When I tried to run the game, I got an error message (Unknown Error: -2147483639) and my laptop's microphone turned on (?!?!). Now the laptop's built in microphone doesn't even appear on my drivers list. I can still hear the sound coming from the microphone. What should I do? I just want to get my computer back to normal.

It's an odd issue... Never seen that before...
What you can try (but I don't promise it'll work) is to do a system restore:

here

Note that it restore the state of the system at the restore point meaning that if you installed a driver, you'll have to reinstall...

It won't erase your files though... So you wont lose any work/art/saves or whathever you did...
Anyway if it's a driver issue and you restore before, the problem will be fixed

I'm having this problem as well, noone found a solution yet?
And thanks for trying to help Azraal, but I don't think anyone will do a system restore as the first option when they don't even know what's causing the problem.

6 months later I`m having the same problem (not the microphone issue but the error, yes) in Windows Vista and this is the only one!!!!! result that Google returns (I think it's the first I see). Help please!

I had the same problem (with the microphone) but i was able to fix it by reinstalling my notebooks audio drivers, hope this helps

i had that problem only if i choose resolution different than 1024x768.

I had the same thing with the Unknown error, and the problem turned out to be redefining the keys. I have to use default keys to avoid the crashing.

I needed WASD controls, so I selected the Default Mouse controls from the control menu (nothing else), and no more crashes.

Thanks a lot for the advice man!

That always-on microphone bug was driving me crazy, and that totally solved the problem! Well, I won't touch that game with a 10 foot pole, unless that issue is fixed...

No problem, the system restore is an easy way to restore your computer state, especially since restore points are pretty frequent if you don't modify the options...

Well it's like hitting a nail with a sledgehammer though...

As for the control problems, as an avid numpad user I usually have a lot of problems with keys (wasd being the standard, numpad tends to be unmappable in most modern games)...
My universal solution for key related problems is programs like glovepie that permits you to map keys to other not the ideal solution but it always works for me...

Massive necro, but it's relevant to the topic.
The D3D version of Messiah has an integer overflow if you have a desktop resolution of 2560x1440 or higher. It'll throw the same error message in your face as OP described. (notice how it's a few bytes off from the maximum negative value a 32-bit integer can hold)

Lower your desktop resolution to 1080p or run the GoG default nGlide version. The nGlide version actually works out really well for Messiah, so I recommend sticking with that rather than fighting the D3D version of the game.