After a very long hiatus, I have decided to play Morrowind again. This time however, I thought I'd try to enhance the game with some mods. I know for certain that I'll be using the MGE, but I was wondering if anyone had any suggestions for mods in general that don't mess up the lore, but provide a better game, such as graphical improvements or mods that change the incredibly aggravating level-up mechanics, etc?

I'm personally a great fan of the Divine Domina series, Balmora and Vivec Expansion (Though Balmora Expansion has a few non-lore-correct armors and such)

And...-checks her ini.file-

Vampire Embrace and scripted spells are a must-have if you want to play as a vampire.
Feminized robes by CanadianIce with meshes by Nioliv (finally found it!)
Children of Morrrowind
Better Bodies
White Wolf of Lokken Mountain (even if not lore-friendly, it's just an awesome mod)
Key replacer
Real Signposts
All boat ports
All Silt Strider ports
No glow (on enchanted items)
Key replacer
Gold replacer
Cliffracer-killer
Slof's Better Beasts

I think that's it, really. There's also something out there (Try Google) called "Telesphoro's List o mods." Great reference-list, and else, try elricm.com, planetelderscrolls, or tesnexus to just browse around.

http://www.gamesas.com/index.php?/topic/1060141-mod-recommendations-for-new-players/page__p__15392814__fromsearch__1&#entry15392814 is great for getting yourself oriented with mods again, and grabbing the most recent patches and tools.
Also includes a link to the GRAPHICS thread, which is really helpful.

http://www.gamesas.com/index.php?/topic/1089101-texture-replacers-of-the-vanila-flavour/ also has some helpful links for finding new textures. (including Connary's work, which is my favourite)

You'll likely find http://www.mwmythicmods.com/Gluby/Gluby_Main.htm very helpful, especially when picking which mod to use for improving the leveling-up mechanics. (I recommend http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=2030)

There are two important leveling mods that I have used extensively; GCD and Madd leveler.

I should add that I've gone back to the vanilla system because leveling mods now seem a little cheat like to me.

Anyway, both these mods work well and have a strong fan base. GCD is a total overhaul and provides seamless leveling with attributes calculated from skill progress.
Madd leveler is more like vanilla but it gives attribute increases on the fly instead of at the level up screen, which is limited to three 1 point increases.

I've not done an extensive search, because I am not a GCD user myself, but the link given by pluto leads to ver 1.7c

Unless I am mistaken, there is a 1.80 verison now, which you can find http://www.mediafire.com/?ylyn2fwmofz As started before, I did not research it in great detail, so there may be a reason Pluto pointed to to an older version, but 1.8 looks legit. (note the uploader's name) Just thought I would point it out in case it got overlooked.

Those links that Pluto mentioned are a good start for you.
If you want to search for mods there is Yacoby's http://search.yacoby.net/ and http://search2.yacoby.net/ (beta) at your disposal too. :user: