Great thread! This was certainly a debate between many of us growing up (I'm old). Lots of great opinions in here as well.

For me, it comes down to Metallica was the better band.  Their albums get progressively better up to Master, which is their melodic peak to me, and Justice is their thrashy best.  But once the black album arrived...eww.  I remember my friend and I watching the world premiere of Enter Sandman on Mtv and, no sir, I didn't like it.  Other than the excellent production quality, nothing impressed me about this album.  But "Metallica" is freak'n Mozart compared to the albums that came next.  :/

Megadeth didn't have a great start in my opinion (the first album is terrible) and other than a few ok songs like Peace Sells, they really weren't anything special through their first three albums... and then it happened.  Rust in Peace is one of my favorite albums of all time from any band.  It's like the two Daves getting together with Nick and Marty for the first time just opened a floodgate of creative ideas or something.  Seriously, you would have to take the best 8 or so Metallica songs and put them all on a single album to rival Rust.  Granted, Megadeth's following albums weren't great but at least they didn't turn into the embarrassment that Metallica did.

Rust in Peace is the best thrash metal album of all time, by a pretty healthy margin.  I'd say that every song on that album ranks in the top 25 thrash songs of all time. Many of them in the top 10. There are at least three on there that I could argue deserve the top spot. 

The first four Metallica albums are all great. The first four Megadeth albums are great too. But, of those eight albums, Megadeth has the best with RIP, and the worst two with Killing is my Business and So far So good So what. After the early 90s albums, both of them went to shit. They have both put out some really bad music over the last 25 years. Both have some recent(ish) stuff that's all right, but a lot that sucks.  Over the last 25 years, there's more Megadeth that's good than Metallica, but that's not saying much. 

Anyway, Megadeth wins in my book. Rust in Peace is such a good album that they would win even if that's the only album they ever made. 

All these years I never noticed that's the acronym of Rust in Peace, I feel so stupid

edit: holy shit it literally says "Rust" in Peace. I'm too dumb wtf

Countdown to Extinction is better than the black album.

I don't think Rust in Peace is even the best thrash album from 1990, let alone best of all time. Coma of Souls is much, much better, and Seasons in the Abyss has it beat too.

I'm not sure (m)any tracks are going in my top 25 either.

I recognized Metallica as greatest in Ride the lightning through Justice for all. After that though, Megadeth was better in Rust in peace through Youthanasia

I’m not a metal fan... and it’s been years since I listened to any of this music. But Metallica, easily. But I’m not particularly familiar with Megadeth. The only Megadeth song I even know of is a cover of Black Sabbath’s Paranoid.

That said, my taste in Metallica began and ended with the Enter Sandman album with two exceptions, both covers: Turn the Page and Whisky in the Jar—while I do like Thin Lizzie, and respect their version more, Metallica’s more piratey sounding cover was more to my taste.

Load is such an underrated album. As I got older I found myself listening to it much more than Kill em All or Black Album

There definitely is nothing close to universal agreement on what thrash is the best thrash. I realized this about 20 years ago when I found out that a lot of people don't even think Rust in Peace is the best Megadeth album. Many people put Peace Sells in that spot. To my mind, this sounds completely ridiculous. For me, Rust in Peace is the best album of any any genre ever made by anybody.

That said, if you surveyed 100 metal heads and asked them what the best thrash album of all time is, Rust in Peace would be a high vote getter. As would Seasons in the Abyss. Peace Sells, Master of Puppets, Ride the Lightning all rank up there as well I don't think many people would put Coma of Souls at the top, but I can see how you put it up there. Bonded by Blood, Reign in blood, and Among the Living are also likely high vote getters. 

I don't know if you ever go on the metal-archives forum, but for the past few years they've have a mid year poll where they vote on a particular topic (eg best album of the 90s, best black metal album). They haven't got round to doing thrash yet, but I'd really like to see it because, as you say, there's so many different opinions and contenders. You sort of know what'd be in the mix, but it'd be interesting to see what comes out on top.

Rust in Peace comfortably won their best of 90s poll BTW.