In terms of counters, since a few mentions went out Shedinja, I should just point out that Sandstorm downs it in one hit, and it's almost always active when Excadrill is in play. Cofagrius' Mummy ability ruins Excadrill, making it a viable switch in. Sableye's Priority Will-O-Wisp and Trick ruin Excadrill. Rotom-W and Rotom-H both work wonders with their exclusive moves.
And since we're discussing Ubers, lets talk about some of the threats he has to contend with there:
Mewtwo: Aura Sphere, Grass Knot, and Flamethrower all hit Excadrill for Super Effective damage, and Excadrill needs Sand Stream in order to hit first.
Lugia: Walls him fairly well, but needs Hydro Pump to fight back.
Ho-Oh: Nukes it with Sacred Fire, as long as it's Sandstorm is out of the picture.
Groudon, Kyogre and Rayquaza: All three of them negate Sandstorm and 1hko him.
Latis: Grass Knot does solid damage to Excadrill, and pack Earthquake immunities.
Deoxys: Superpower, done.
Dialga: Aura Sphere. It should have something to take down Sandstorm on it's side though.
Palkia: Aura Sphere or Surf boosted by Rain Dance should down it.
Arceus: Arceus has a lot of ways to hit it, but most of the main sets it runs don't exactly cover Excadrill, so he might have an edge here.
Darkrai: It needs Sand Stream to outrun Dark Void, but Darkrai doesn't have much else to use against Excadrill.
Giratina: Aura Sphere and Earth Power work well, and it has Will-O-Wisp.
Shaymin-S: Seed Flare can gun down Excadrill, unless it gets in Rock Slide first.
Zekrom: Excadrill can wreck Zekrom with STAB Earthquakes, and little fear of it's retaliations.
Reshiram: Reshiram on the other hand, can annihilate Excadrill with Blue Flare.
Thundurus: Thundurus needs Grass Knot to hit Excadrill, and it doesn't always carry it. Excadrill is immune to Thunderbolt/Thunder and Thunder Wave and can fire back Rock Slides.
Basically, most stuff there can handle hit or counter him. Thundurus, Zekrom, Darkrai may be the only real exceptions, but even then, Darkrai can put it to sleep. He won't do too well there.
This is a signature that doesn't eat up an absurd amount of space.