Sol Badguy: His real name, (Frederick) last name, (a reference to "Mr. Bad Guy") and even his theme song ("Keep Yourself Alive") are some of all the references to Freddie Mercury and Queen in general (to hammer the point home, his head-plate has the words "ROCK YOU" engraved on it). It helps that hisVA (Daisuke Ishiwatari, also the man behind the game) is a huge fan of Queen, something you'll see in this entire page.
A relatively subtle one—his sword technique is clearly inspired by Mercury's theatrics with the top half of a mic stand.
Axl also takes cues from Billy Kane, from his dress sense (bandana, Union Jack-pattern shirt) to his fighting style (long-range pokes, counters, "leap-off-the-screen-and-dive"-attack, flaming weapon spin Overdrive).
Justice: One of her Overdrives is called "Gamma Ray".
His Xrd redesign bears a striking resemblance to both Alphonse and Panzerfaust. He even has the letter "Z" emblazoned on his shirt, possibly referring to Mike Zaimont (Skullgirls' creator and former professional Potemkin player).
Millia Rage was named after the metal band Meliah Rage.
Very deep inside, her surname may be a reference to the metal band Rage as well.
Zako-Dan of Isuka might have been inspired after Team Rocket.
Specifically, Zako-C is an Anime Chinese Girl who not only has clawed gloves, but also wears a Qipao that doesn't cover her back and has Odango Hair... Sounds a bit familiar, doesn't it? Well, one of her palettes you get to see during GG Boost even makes her look perfectly like an Alpha Chun-Li.
Overdrive, basically GG-ese for "super move", can be seen as a reference to the guitar amplifier effect of the same name. note It's the one that goes CHUGGA CHUGGA CHUGGA.
Gig, the boss of Guilty Gear Dust Strikers is classified as a Megadeth-class Gear.
Some texts in Accent Core Plus uses Metallica font.
Bedman, the new character for Xrd, is named after Bedemon, a side project of heavy metal band Pentagram.
His white hair and glasses look could possibly be a reference to Kabuto Yakushi.
His ability to trap people in nightmare worlds of his own creation is a direct reference to Freddy Krueger and Death 13.