Ahhh, good discussion this is!
To the newcomers (Carlos and the other chap): Really, you should not be afraid to clean your mods! Again a good starting point are the "dirty" and "clean" lists that are supplied on the CS Wiki. Over the last month or so there has been a pretty good effort going on to update and verify them, with Thomas Kaira one of the key contributors.
A Big Thank You for Thomas!
I think Thomas will agree with me when I say that all mods on the "need cleaning" list do not have implicit dependencies and are therefore perfectly safe to clean with the automated process as outlined in the Guide (finding ITM's and UDR's).
I view it this way: Faced with choice of not cleaning your mods at all because of fear to screw up, especially if they are listed as "need cleaning", or do clean and possibly run into an issue with a chance of 1 in 200 (maybe) I'd say DO clean. Not the least because if there should be an issue Tes4Edit always makes a backup copy of the plugin. And you should keep copies of all original mod downloads anyway. So it's always easy to revert to the unclean version.
The process of cleaning as per the Guide is easy and quickly done. It just requires a bit of time, mostly waiting for the PC to finish the processing and filtering. It's perfect for doing on the side while surfing the net...
And then there are always the forums / this thread: if in doubt just ask. Chances are someone before you already has experience with it and can guide you.

So in summary, there is really no reason not to engage in cleaning mods yourself... :grad: