Mods like Dim and Breeze, and those that increase the textures of landscape, etc. are
replacer mods, they don't show up in FOMM, they merely replace default meshes/textures in the Data sub folders.
In the mod load order, I tend to group mods this way in FOMM:
1. Master files (.esm) - beginning, of course, with Fallout3.esm, then the DLCs, then mod-specific .esm files.
2. Minor game mechanic mods. Things like No Karma messages, No VATs, No Fast Travel. Since these types only change a few (or one) game setting value, they are usually safe to put up top. If they do get conflicted, it's an easy matter to restore their setting in my merge patch in FO3Edit.
3. "Fixer" mods. This type of mod fixes a certain nerfed aspect of the game. UrgeRivetCityBridgeFix, PandorasBox, FixHaleyRepair all fall in this category. Like the preceding, they generally touch a very limited aspect of the game and if conflicted with other mods, can be easily accounted for in my merge.
4. World-Altering Mods. These mods make massive changes to the Wastelands or the game mechanics. Mods like Fellout, Arefu Expanded, Shady Sands, DCInteriors, CEI, MMM, Enhanced Weather all fall in this category. Over time I've gotten a feel for mod conflicts and this is my "probably will conflict with someone else" category. I order them so the ones that use major scripting follow those that are don't.
5. Adventure or quest mods. Mods like Puce Moose's An Evening with Mr. Manchester, A Note Easily Missed. These mods tend to be pretty conflict-free (as long as you stick with mods that obviously don't impact the same area). Small conflicts are resolved in my merge patch.
6. NPC mods. Those mods that make changes to the NPC(s) in the Wastelands. Better Caravans, Lings Pretty Things, JHBCloverPlus fall in this category. I order them from general (LPT) to specific (JHBCloverPlus). Conflicts here are generally of the cosmetic sort and the last-loaded "wins," though my merge patch can tweak that so the winner in a particular record (like facegen) is whichever one is more aesthetically pleasing. Sometimes there are aspects (Essential, level 30 cap with Broken Steel) that you have to watch out for, so they don't get overwritten.
7. Custom race mods. Things like playable Tribal, playable_as_old_raider_ghoul and Alternate Start - Roleplayers fit in here. Conflicts galore, but generally not fatal. Mainly it is setting these mods to play nice, remove the Playable flag on those races you don't want to play (kids, in my case) and adding LingsFinerThings - Coiffure as a master using FO3Edit so that customized hairs, eyes, etc. are available without conflict, with any racial conflicts resolved in my merge patch.
8. Armor/Clothing mods. With the exception of Lings Finer Things, which modifies Tenpenny Tower, so it precedes this category. Mods like Tailor Maid, DLC03_Hellfire, Missing Unique Amor Enhanced, Binoculars and Scopes, AzarGypsyOutfits all fall in this category. Again, I order them from general to specific. Some minor conflicts here (like weight and AR value conflicts with realism mods), but they are easily fixed in a merge patch.
9. Realism Mods. These mods impact the nature of the game via scripting or game setting changes. They are here so things like Arwens_FULL_Tweaks, Survival of the Fittest, etc. can do "their thing" and win most conflicts. Script and other mechanics conflicts are quite common in this "category" and by putting them near the bottom, they are most likely to override favorably. Script conflicts are the most common in this group.
10. Things That Really Need to Load Last. Some mod authors insist that they load last, so here I try to accomplish that. Often, as I'm testing, they begin to creep upward in my load order. Mods like NPCs Sleep Tighter, Rude Awakening, corrected weights clutter, WeightAmmo fall in this category. And of course, my merge patch loads last.
Hope this helps