flats have a better fundamental, so it cuts better in the mix and provides more rumble instead of the clank that rounds provide which, presumably, is something you want in a doom band
The higher tension could also come in handy with the extreme downtuning and all
In combination with fuzz pedals, though, Rounds add some much needed bite to the tone. YMMV.
Now, to be helpful instead of pedantic:
So, you want to set yourself up with a Doom Rig.
Sanford&Sonny's right on the money, you want lots of speaker area, you want as cheap as you can get, and you want at least one distortion pedal (Muff or not, it really depends on what your guitarist (if you've got one) is doing).
For example, Al Cisneros gets away with a DOD 250. Very clearly not a muff-based-fuzz, but his tone gets absolutely swallowed up if you've got a guitar going.
With a guitarist, the most important thing is that the two tones complement each other. Since 90% of the time you're going to be playing the same riffs, its very high priority to make sure the tones blend together. Check out High On Fire's Surrounded By Thieves... There's not a lot of low-end on the guitar, but the bass is more than providing for it (and, actually, the album is incredibly bass heavy). In a situation like that, you want a really thick, low-mid heavy tone. That way, when Pike takes a solo, the sound doesn't empty out.
The other important thing is volume. Since you're dealing with a lot of whole and half notes, you gotta have the thing sustain. It also better be loud. A big part of doom's evolution was the stupidly loud amplifiers from the 70's, and figuring out what to do with all that volume.
Unfortunately, those tube amps have seen a dramatic rise in price over the last three or four years. If you want to do this on the cheap, you're going to end up scouring Craigslist for Peavey stacks, Kustom stacks... anything with four or more 10"s or two or more 15"s. You can get Peavey 2x15" stacks all day long for +/-$300. Not to mention, a lot of those heads have their own unique sound. They don't sound like melting tube amps, but they've definitely got something special about them.
Just keep this phrase in the front of your mind: Shake & Bake.
You want your sound to shake the world, and you want those who do imbibe to put your record on whilst exploring the outer-limits of consciousness.
Doom on, homey