Okey i have too much time right now so here is what i did:
- I installed trackercfg
- Added one of my albums to nowatchfolders
- Opened media player and looked albums. Everything there
- Close all apps (except trackercfg)
- Tapped trackerxfgs top menu and chose save
- Tapped top menu and chose "rebuild databases"
- opened xterm and run command top
- Watched tracker processes to go from 10-60 % cpu for about ~5-7 minutes and after that thumbnailerd process kicked in and did same thing (i do have very little media on my N900 so if you have full of video&audio the tracker process could probably run for 30 minutes at least)
- After those processes went away I opened media player and there was no album what i added to no watchfolder

So...Just for you

Thanks slender. Could do successfully as per your steps.

However, in media player few files name given below continue to be shown. Do you have any clue where they are located :

modular
ring
ding2
whistle
beep
phone
ding
phaser
vibe
setsound

I seems to have added all ringtones folder to nowatchfolders. However, dont know where about files are hiding. Please help me to figure out which more folders I need to add to hide all these files.

Thanks.

These files are not ringtones they come with sygic navigator.
to remove them from the playlist add the following to the nowatchdir

./home/user/MyDocs/Res/

I've located these files using this command in the therminal
eighter on the phone or through ssh

find -name wishtle*.*

these files were in MyDocs/Res/sounds/ but there are also files in MyDocs/Res/voices/