Yes. Don't click Just Fix It.
That'll create a Merged Dialogues plugin. Whilst a valiant attempt by Ghostwheel it in fact causes more trouble than it fixes.
Merged Objects is fine (although it has been known to bork when there're lot of objects needing merging).
Merged Lists (I think that's what it's called) needs a second tool: Aerelorn's levelled list resequencer.
The Just Fix It command will also clean your active plugins. I'd recommend (for safety's sake) ensuring that Restricted Dialogue Cleaning is enabled in Options.
If you're just after cleaning mods I'd recommend tes3cmd (and that will create a merged levelled list plugin as part of its multipatch feature).
For levelled lists you're better off with tes3cmd or Wrye Mash's Mashed Lists (just for not needing a Resequencer, as long as you use that with TESTool you should be fine).
What cleaning does is to compare a mod's records against those in the relevant ESM files. If a record is the same as in one of the Morrowind masters then that record can be removed. TESTool will also clean out empty cells. Read the TESTool readme which gives some ideas as to when its cleaning could be a bad idea, and the options are available for you: Restricted Dialogue Cleaning and Restricted Cell Cleaning.
@ eldrig: Which mods should not be cleaned? I think there's a lot of FUD about that.
[Edit: http://code.google.com/p/mlox/wiki/Tes3cmd#multipatch_-_Patches_problems,_merges_leveled_lists,_etc. and something I didn't mention: Era Scarecrow's http://www.gamesas.com/topic/1367045-smartmerger-3/ which can apparently duplicate TESTool's Merged Objects functionality without falling over. I haven't tried SmartMerger but have used tes3cmd quite a lot, yet to run into any problems].