I didn't have any trouble getting this to work either.
Installed EQ plus expansions, ran everquest.exe which downloaded like 1 file, then clicked the 'Optional' button, some more stuff happened, was asked to restart everquest.exe and finally some real patching started.
30 minutes later (or 1 night for dialup modems

) I installed the EQemu patcher to the everquest directory and ran it (good thing it has a desktop shortcut...with 1000+ files who'd find the right executable anyway...off course somewhere the filename is mentioned

- oh and i had the EQLive patcher check the files).
Even though the missingfiles.log was as good as blank the eqemu patcher complained about 5 missing files which caused me to locate those files on Sony's server to get get the patcher to stop complaining

(BTW where the heck does discard.log come from, its the only file left listed as missing in the eqemu patcher)
The game runs just peachy, played 15 mins on foreverhacking through router and zonealarm.
The only thing that didn't work was the tutorial which reports some crap about a missing link in some dll file.
Unfortunately the joy was shortlived...does EQ suck or what (my appologies to the fans

).
I thought Ultima Online graphics were kinda way behind the times, but EQ graphics are like the original Doom (go download that and see how ugly that is...pretty much the same as EQ :P ).
Can't even save the day at HIGH res on my 19 inch sony monitor (GF3).
The human starting city Quiznos (actually Quey something...) has the worst layout I have ever seen in any layout of anything in anygame...the thing is like a labyrinth...after 15 minutes of walking around I didn't manage to find any exits to the city that didn't drop me into the ocean, none of the NPC has anything to say (you go hail and they ignore you), you get 1 food ration and 1 milk skin (from the help I gather you are supposed to get 20 of each)...and to make things worse I got so motion sick I had to stop :P
This is officially the first ever game to make me motion sick :(
(Doom, Quake, Unreal, Unreal 2, UT, UT 2k3, MOHAA, RTCW,BF 1942....and so on...none of them even remotely make me motion sick :P - it's those damn ugly textures I tell ya :P)
I thought the PS2 version looked back, but at least the character models aren't life sized
Anyway all I wanted to really let you know is that as of this date EQemu does work with the latest patched version of EQ.
To all those who can't get it to run: it really isn't worth it.
(now I gotta play a game of solitaire to show my eyes what decent graphics look like

)