While Factory (along with other cult labels from the 80s - Mute, Rough Trade, 4AD, Creation, etc.) will always get over-praised and like each of the afforementioned labels released their own stinkers (see To Hell With Burgundy), I would tend to say that Factory had some landmark releases outside of the Joy Division/New Order crew:
Section 25 - Looking From a Hilltop: predated acid house by four years (nice sequencing job Barney!). Still a relevant song today.
ESG - You're No Good: no-disco at it's best, sampled by everyone and their mother, a Larry Levan classic!
A Certain Ratio - Do the Du, early works: though they eventually fizzled in my opinion, their early works are seminal at best. See The Rapture and LCD Soundsystem.
The Durutti Column: what else can I say, Vini is a genius. See Vincent Gallo's "When" LP to see his influence.
Happy Mondays: Sorry, but the Mondays deserve some cred. They were the first to integrate the acid house vibe into rock music. They worked with Oakenfold, Osborne, and Weatherall before they were cool - well before folks like Primal Scream clued onto this and ran with it.
Records by Cath Carroll (her album still stands up today), Quando Quango, The Wake, and Marcel King were also superb. Not to mention the fact that they launched the careers of James and OMD. They also supported folks like Cabaret Voltaire.
Because of this, I can forgive them for To Hell With Burgundy and mediocre acts like Adventure Babies and Northside.