Keep in mind that you also needed a Linux system to use SEQ. And if I remember, it wasn't the same computer you played EQ on. It just acted as a packet sniffer.
Most high end guilds didn't cheat (outside of seeing boss stats with SEQ) because GM's would absolutely watch and make sure you didn't cheat. In Enlightened Dark (My guild from Tarew Marr), one of our officers was a programmer for the SEQ team. Well, he never confirmed that, but it was definitely an inner-guild rumor, and we know that he ran SEQ on raids because he would tell us how many HP bosses had or what not. I know that Ashran, the SEQ creator, was a Necro on Tarew Marr, but he was never in guild.
Anyway, aside from having SEQ to know various info about a boss, there was no "cheating" per say. I do remember when Lost Dungeons fist came out, there was a cheat that allowed the in-game map to work similar to SEQ in that it would display the location of every mob currently spawned in the various dungeons, and would show them move and stuff. It was really neat. I don't remember if SOE fixed that, or if someone (not in our guild) got banned for doing it, so I think that I got scared and removed that ability from my client.
EDIT: Scratch that, I do remember that EQ had a few dupe bugs in the day. Somehow there was an invisible banker in Befallen that would dupe shit for people. Someone in my guild found out about that one. Then in Luclin, there was another dupe bug using stackable items. If an item was stackable, selling a single item to a vendor would allow you to purchase a full stack back from them. Yes, it cost a lot (vendor prices were always high), but using that method helped me go from like 50 tailoring all the way up to 225ish. Then I got the remaining 25 points making those robes for people to use on the earring quest.