I take no responsibility if you brick your phone or whatever, This is what I have done, maybe there is a better or more right way witch I will gladly learn if someone think this is wrong in any way. This worked for me and I have done it several times on my own and friends devices.

I have done this with Windows Xp. And when you do this remember this will COMPLETELY reset your phone to factory settings everything will be lost if you haven't done backup. I recommend you to download and install Nokia Ovi Suite and do your backup of contacts and sms from there. I haven't done backup of my mms, if you want to do that you have to search the web because i dont know how frals fMMS store the mms files. Don't use Nokia Ovi Suite to backup files and photos because it takes forever and you can't see what the f--k it's doing. Connect your phone using the usb cable in PC sute mode. Choose the tools menu and backup, uncheck everything that isn't contacts and sms, do the backup in Ovi Suite. Then disconnect usb and connect again in mass storage mode. Now backup everything else such as .video .images DCIM or anything else you want to backup with your choice of file manager. The memory card you simply remove from the phone until done.
Now then when your are done and have a fully loaded battery or at least half:

First login with your IME number (under your battery)
http://tablets-dev.nokia.com/nokia_N900.php

Download the eMMC file:
RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin
And then download the correct file for your contry. mine is for Europa:
RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin

Then you download the Flasher command line tool here:
maemo_flasher-3.5_2.5.2.2.exe

Save everything in a folder so you know where everything is.

Now simply install the maemo_flasher by klicking on the maemo_flasher-3.5_2.5.2.2.exe file and follow the instructions.

When done you go to the Maemo folder C:\program files\maemo\flasher-3.5\ Copy the two files you downloaded to that folder.
The eMMC file:
"RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin" (same for everyone regardless of the contry you are in)

Then copy the firmware file, in my case it's:
"RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin"

This is done because it's easier to run the flasher with the files in the same folder as the flasher program, you can delete the eMMC file and the firmware file in the program folder when you are done if you want.

Now turn off your phone, wait until you are sure it's done. usually takes 3-5 seconds.
Hold the "u" key on the phone and plug in the usb cable. You can let go of the key when you see the Nokia logo and the little usb symbol up in the upper right corner of the display.
The phone is now in flash mode.

Windows will now automatically detect new hardware and install it. Wait until finished, don't take long.
Open up start menu in windows and choose run, then run "cmd".

Now in the cmd (Windows Command line window) go to your flasher-3.5 folder. Mine are in:
C:\program\maemo\flasher-3.5\

When you are in the right folder type:
flasher-3.5.exe -F RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin -f

The flasher will now flash the eMMC, wait for it.

When done this is important: This worked for me (several times) unplug the usb cable DO NOT TRY TO START THE PHONE UP remove the back cover, remove the battery and wait 5 seconds. Replace battery and cover, again hold down the "u" key and plug in the usb cable and wait for the Nokia logo with the little usb symbol in the upper right corner. Then release the "u" key.

Now in the cmd window on your pc type:
flasher-3.5.exe -F RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin -f -R
or replace the "RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin" part with the firmware file you have downloaded.

The phone will now flash reboot and startup. You now have a freshly installed operative system.

Part 2: writing it now.