Phi Kappa Phi is a national honor society, allegedly the "nation's oldest, largest, and most selective all-discipline honor society", whereas Phi Beta Kappa is the eldest of all honor societies, but it only applies to liberal arts. And, of course, not all univiersities have Phi Beta Kappa (mine doesn't!), but then again, not all have Phi Kappa Phi either.
Phi Kappa Phi's national site indicates the top 10% of seniors & top 7.5% of juniors are invited, along with the top 10% of graduate students. However, local chapters can have more stringent requirements. For example, my university only invites the top 5% of juniors (vs. 7.5%) and "outstanding" graduate students determined by who knows what (or who!). I believe they (local chapter) look at some other criteria but unsure what they really are, other than nomination by faculty. Phi Beta Kappa's nominate the top 10% of undergrads, although once again, chapters may have more stringent requirements or other criteria to meet on top of this.