I have mods I would like to play that require each of the three big extenders. How do I run them all at once with the minimal amount of lags, crashes, and explosions? Which should be run first?

I am unsure about MWE, since I've never used it, but if you have MGE then you do not need MWSE (it has it's own MWSE within it)
That solves half your problem.

Actually, Im not sure about updates for MGE, but I used its internal MWSE and then tried using MWSE separate, and got a small but noticable boost to fps.

i suggest running the newest beta version of MGE (v3.8.2 rev 178) or if you dont want to play around with the beta, use the newest stable version (v3.8). that should solve the MGE MWSE problem, and then i guess you could just run MWE also? never used it so i dont know anything about it.....to tell the truth i dont even know what it is, or maybe i do...(morrowind enhanced??)

i used them all!!!! yeah!!!
like so:
setup MWE to launch to MWSE worked great, but seeing as u have MGE, u just need to have that setup, and launch with MWE.

atleast thats what i can tell, unless you mean something else?

I thought that MWE and MWSE were incompatible?

Nope, perfectly compatible, though I use to have some problems with saved game corruption when I used to use MWE, even with the patch from MCP, which is why I stopped using it and its associated mods, supposedly there are work arounds for the corruption, but it seemed like too much effort to make sure that I could load a saved game, so I dropped it.....though there are some pretty sweet mods for it that improved gameplay quite a bit.

To be honest, I'ld just like to see some of the popular mods that are available for it, like the blocking enhanced and oblivion style spellcasting made as patch options for the MCP instead, but I honestly have no idea what type of effort would have to be involved for something like that.

I use all 3 in perfect harmony. I usually open MWE, and switch the launcher to MWSE. If I need MGE I just set my options and close it, and it works pretty well.

I just installed everything yesterday and I use launch Morrowind from MWSE, and then MWE and run the game and it works perfect. Probably should be the same if you also add MGE in it

I agree, and add combat enhanced to that list too. Combos are sweet. But maybe someday these things could be incorporated into something more stable like MCP.