So, I've managed 280,143 with Ganondorf. It was a perfect 6x1000, to boot. Got a good Sneaky Spirits Fest (those are almost better than Souflee Fests, since they always drop All+ icons), and completely annihilated at least 2 Clubberskulls.
My loadout:
Equipment:
Critical Hitter Brawn Badge (+7 Atk, -40 Def)
Mysterious Magic Stone (+78 Atk, -43 Def)
Air Piñata Cape (+85 Def, -16 Spd)
Strategy: Pure power for Ganondorf. He's slow as molasses already, but with his defense, he can afford to use an Air Piñata defense item, chosen for its ability to make up the defense lost by the Attack equips, while not penalizing Speed too much. Critical hits come in VERY handy when using Spinning Blade, or other Smash Run Powers that deal damage.
Specials:
2 - Warlock Blade
1 - Flame Choke
3 - Dark Vault
2 - Wizard's Dropkick
Not much to say here, but Dark Vault makes some early climbs MUCH more bearable. The others are just good for him in general.
Powers (30 weight):
Strong Kick Lv. 3
Super Armor Lv. 2
Spinning Blades Lv. 2
Back Shield Lv. 4
Health Recovery Lv. 2
Back Shield Lv. 1
Power Strategy: Back Shield takes advantage of the fact having a worn item attached passively raises Arms. Five uses plus your pickups usually means you have that stat maxed almost every time. Spinning Blades comes in handy for early Enemy Squads, or ones that have lots of shielded enemies or Gastly. Also pop one for Sneaky Spirit or Souflee Fests (I've snagged half a dozen Souflee kills in one such Fest already). Super Armor and Strong Kick are meant for the really tough enemies (Clubberskull, Polar Bear, Bonkers, Bulborb and Reaper mostly), and generally work as a team. Pair the Strong Kicks with Critical Hits, and you can easily kill even a Clubberskull in just a few Up Smashes. Since you're right in the thick of the fight throwing melee attacks left and right, you're going to take a lot of damage, and that's where Health Recovery comes in. It's better to save that until later, as it will recover more, but use it when you need it.
Run strategy:
When to quit out: If you die, if you get Warp after defeating a massive enemy but before you can collect the boosts, or when it's just going bad in general. Use discretion.
Early game: Ganondorf can't move around very easily. He's slow, can't jump too high, and Dark Vault is kinda slow. If you start high on the map, STAY high until you start getting better Jump and speed stats. Ideally, you want to work your way across the top of the main island and take the platforms up further. Avoid doors early on. nothing sucks harder than getting the Hard Target Smash when you're fresh, and slow as hell. You just won't do it, and you'll waste close to a minute with the loading and failure, with little to show for it. Just pop your Back Shield instantly, and when it drops, pop another one on.
At this point, even Mites will be dropping decent-size stat boosts, so if you see a gang, wreck them. They seem most efficient at this stage. Don't be concerned about grabbing all the little Attack or Arms icons, as you should be getting a bunch of Attack and Arms naturally. In my experience, though, focus on: Speed, Jump, Special (ALWAYS focus on special; you won't be getting much from use) and Defense.
Also take note if you see a Souflee or Sneaky Spirit in the more difficult areas. If you do, keep watch on the timer bar for the white event lines. Any Fest events will use enemies that already exist in the map, so if you don't see Pookas, Tiki Buzzes or Bullet Bills, but DO see those two, you're in luck.
Mid game: Get a feel for how your drops have come out, and start focusing on deficient ones. If you're close to an Event and near a narrow hall, get there as soon as possible. If it's a Souflee Fest, you've put yourself in the best possible position to rack up kills (as they won't go through solid walls). Anywhere else, or on a Sneaky Spirits Fest, pop a Spinning Blades and aim for the densest area you can find. If you get Amped Up, start ascending the central shaft since you can do that for free. If you're near a door and you get Gust or Shrunk, consider entering it to break the effect early. Depending on the enemy, go to the Wanted area and take out that bonus enemy for 3-5 BIG boosts.
Late game: By now, you should be in the 600-700 range on Arms, Defense and Attack, and close to there in Speed and Jump if you've been diligent about collecting those. If you've had a good bonus Fest, those are probably closer to max. Keep focusing on Special and Defense, and head to where you generally find the heaviest of enemies. By now, even a Clubberskull will feel your wrath in just a few seconds, especially with Curry, or a Spinning Blades active for extra time between attacks. Pop a Strong Kick if you have one left and go to town.
Pickups: Depending on how many smash Powers you already have (I have all but one that needs a challenge to unlock), you can forego collecting them, but always grab custom equipment. I usually prioritize those and Gold coin stacks, and get Silver when I can, ignoring Bronze unless it's right there.