I have uninstalled some big mods (MMM, FWE and Iron Sights). Do you think a clean install of Fallout 3 is also necesary if I want to play just vanila with DarnUI and a landscapes mod?

Clean install? It would be like destroying your house and building it anew instead of just re-painting. If you rally paranoid you could delete all meshes, textures, sounds etc folders from you Data folder although I think that just turning off archive invalidation should be enough.

Check the readme files for the mods you no longer want to use. If disabling them requires more than just deleting/unchecking in FOMM the .esm or .esp file, there should be uninstall instructions included with the readme.

Make a clean save with just the mods you want to use activated (I assume you'd be starting a new game) and see how it goes from there.

You can save yourself a LOT of time by learning to use the Installers tab in Wrye Flash. Don't bother with FOMM; packages are obsolete.