I have a confession to make. I never, until very recently, had any member of the Magmar family in my possession. Mostly due to getting different versions of the game, but the flaming duck has always been kind of elusive to me, which is a shame because I find it to be one of the best designed pokemon in the original game.
When Gen IV came out it followed the footsteps of Electabuzz and pretty much got the treatment it deserved a more balanced, super-powered attacker. While Electivire is more prized because of it's sweeping abilities and more favorable typing (and something I used a lot, mind you.) Magmortar is kind of left in the dust; it has an amazing special attack, but everything else is more average in comparison.
But let's get on with it. Let's look at the tale of the tape!
Abilities: Flame Body (30% Burn Chance), Vital Spirit (Prevents Sleep)
On paper Magmortar is pretty good. The special attack is high in the rafters and Magmortar has access to a LOT of potent fire-type STAB moves in that category, as well as some good coverage moves like Thunderbolt and Focus Blast that take advantage of it's 125 base SpA. It's SpD and regular attack are also pretty impressive, giving Magmortar access to mixed-sweeping capabilities, just like Electivire. Also like Electivire, it's base HP and Def are the same stats, but it's speed that once again wins the day, a decent 83 vs a impressive 95 to it's electric-type counterpart.
It's not all bad though. EV boosts in Speed help the flaming duck to be more viable, and there are a plethora of options to use against opponents.
Magmortar @Life Orb
Ability: Flash Fire
Nature: Timid (+Spe, -Atk)
EV: 16 HP, 252 SpA, 240 Spe
Hidden Power (Ice)
Standard attacking set that utilized the special attack only. The nature and EV's give Magmortar a speed that is in the high 290's, giving it a good shot at taking down slower, more bulky opponents. Thunderbolt is great for bulky waters, focus blast for dark types, and HP Ice for dragons. Of course, Flamethrower for STAB, such a potent STAB that has the power to OHKO Ferrothorn.
Magmortar@ Life Orb
Ability: Flash Fire
Nature: Naughty (+Atk, -SpD) or Naive (+Spe, -SpD)
EV: 208 Atk, 232 SpA, 68 Spe
-Rock Slide/Earthquake/Hidden Power (Grass)
Basically a typical mixed attack set. Spreading the EV's out a bit and emphasizing the raw power of Magmortar to pretty much 2HKO most of the UU/RU/NU field. Fire Blast is such a powerful STAB with Life Orb and high SpA it can rip through opponents, thunderbolt again is standard for bulky waters, Cross Chop can take out special walls, like Chansey, Blissey and Cryogonal with relative ease, and the last attack can change depending on what type of coverage you wish to use. Personally, HP Grass is great for the ground types on the field.
Now there are other options for Magmortar, because the two sets above are the standard fare that you would see. Access to the elemental punches and Fire Blitz for a more offensive STAB are also viable, as well as flame charge which can boost speed quickly. You can also run substitute as a defense and back either focus punch or just spam other attacks in it's place. Mach punch is also viable because of priority, and there are also choice specs and choice scarf options as well. Finally, solarbeam is always worth mentioning for sun teams because it covers all of their weaknesses, but the lack of speed hampers its effectiveness.
All in all, the only problem Magmortar has is it's typing. Because of the mono-fire type, you have the epitome of a glass cannon here. It will hit hard, but it may only have one shot to do so. Revenge killers can easily destroy him, as do most priority moves and stealth rocks. So if used, be aware of it's massive strengths and glaring weaknesses.