JS (node) - 528 468

k=n(2)+'ABCDEFGHIKLMNOPQRSTUVWXYZ',p=n(3),t=o=''
for(i=0;i<k.length;i++)if(t.indexOf(k[i])==-1)t+=k[i]
for(i=0;i<p.length;){a=f(c=p[i++]),b=f(!(d=p[i])||c==d?'X':(i++,d))
if(a.x==b.x)a.y=(a.y+1)%5,b.y=(b.y+1)%5
else if(a.y==b.y)a.x=(a.x+1)%5,b.x=(b.x+1)%5
else a.x=b.x+(b.x=a.x,0)
o+=t[a.x+a.y*5]+t[b.x+b.y*5]}console.log(o)
function f(c){x=t.indexOf(c);return{x:x%5,y:x/5|0}}
function n(a){return process.argv[a].toUpperCase().replace(/[^A-Z]/g,'').replace(/J/g,'I')}

Sample output:

$ node playfair "Stack Overflow" "The cat crept into the crypt, crapped, and crept out again."
SIRACARDFMVUICVSMORDZNAKECMZMFBCYNRDFMSVTVKBTMMY
$ node playfair "Lorem ipsum" "dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat."
CRORSDAHGAMQKPXDOFQMQAMSBSSPUPBPTDMOAHURNRCRLUAULRGNMLCPLSKDSBSBSQQAHMIGRERYMQCROREMAGDTSZIMUHAIAQRQALSGLAHSLZRQPIETAPDXRPNMSFRYMEBPZGHARKIEMIOGROIGREPUHSUPAQIMUHAPUOYRPGRLLRCRKPXDUYAINZ

JS (node) - 528 466

k=n(2)+'ABCDEFGHIKLMNOPQRSTUVWXYZ',p=n(3),t=o=''
for(i=0;i<k.length;i++)if(!~t.indexOf(k[i]))t+=k[i]
for(i=0;i<p.length;){a=f(c=p[i++]),b=f(!(d=p[i])||c==d?'X':(i++,d))
if(a.x==b.x)a.y=(a.y+1)%5,b.y=(b.y+1)%5
else if(a.y==b.y)a.x=(a.x+1)%5,b.x=(b.x+1)%5
else a.x=b.x+(b.x=a.x,0)
o+=t[a.x+a.y*5]+t[b.x+b.y*5]}console.log(o)
function f(c){x=t.indexOf(c);return{x:x%5,y:x/5|0}}
function n(a){return process.argv[a].toUpperCase().replace(/[^A-Z]/g,'').replace(/J/g,'I')}

Sample output:

$ node playfair "Stack Overflow" "The cat crept into the crypt, crapped, and crept out again."
SIRACARDFMVUICVSMORDZNAKECMZMFBCYNRDFMSVTVKBTMMY
$ node playfair "Lorem ipsum" "dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat."
CRORSDAHGAMQKPXDOFQMQAMSBSSPUPBPTDMOAHURNRCRLUAULRGNMLCPLSKDSBSBSQQAHMIGRERYMQCROREMAGDTSZIMUHAIAQRQALSGLAHSLZRQPIETAPDXRPNMSFRYMEBPZGHARKIEMIOGROIGREPUHSUPAQIMUHAPUOYRPGRLLRCRKPXDUYAINZ

JS (node) - 528

Note to the people using the /(.)\1/ regex; that will find all repeat digits, not just those in "pairs".

a=process.argv,k=n(a[2])+'ABCDEFGHIKLMNOPQRSTUVWXYZ',t=o=''
for(i=0;i<k.length;i++)if(t.indexOf(k[i])==-1)t+=k[i]
p=n(a[3]).replace(/../g,function(c){return c[0]==c[1]?c[0]+'X'+c[1]:c})
if((l=p.length)%2)p+='X'
i=0
while(i<l){
 a=f(),b=f()
if(a.x==b.x)a.y=(a.y+1)%5,b.y=(b.y+1)%5
else if(a.y==b.y)a.x=(a.x+1)%5,b.x=(b.x+1)%5
else a.x=b.x+(b.x=a.x,0)
o+=t[a.x+a.y*5]+t[b.x+b.y*5]
 }
 console.log(o)
function n(s){return s.toUpperCase().replace(/[^A-Z]/g,'').replace(/J/g,'I')}
function f(){x=t.indexOf(p[i++]);return{x:x%5,y:x/5|0}}

Sample output:

$ node playfair "Stack Overflow" "The cat crept into the crypt, crapped, and crept out again."
SIRACARDFMVUICVSMORDZNAKECMZMFBCYNRDFMSVTVKBTMMY
$ node playfair "Lorem ipsum" "dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat."
CRORSDAHGAMQKPXDOFQMQAMSBSSPUPBPTDMOAHURNRCRLUAULRGNMLCPLSKDSBSBSQQAHMIGREUUNGROREMLGTTSZSIBYFIAQMHSAGGRSHALYLHSGAYFPUKRANESFRYRODAHGZPLQSRVMIOGROIGREPUHSUPAQIMUHAPUOYRPGRLZRRCPKRKURYFGZ

JS (node) - 528 468

k=n(2)+'ABCDEFGHIKLMNOPQRSTUVWXYZ',p=n(3),t=o=''
for(i=0;i<k.length;i++)if(t.indexOf(k[i])==-1)t+=k[i]
for(i=0;i<p.length;){a=f(c=p[i++]),b=f(!(d=p[i])||c==d?'X':(i++,d))
if(a.x==b.x)a.y=(a.y+1)%5,b.y=(b.y+1)%5
else if(a.y==b.y)a.x=(a.x+1)%5,b.x=(b.x+1)%5
else a.x=b.x+(b.x=a.x,0)
o+=t[a.x+a.y*5]+t[b.x+b.y*5]}console.log(o)
function f(c){x=t.indexOf(c);return{x:x%5,y:x/5|0}}
function n(a){return process.argv[a].toUpperCase().replace(/[^A-Z]/g,'').replace(/J/g,'I')}

Sample output:

$ node playfair "Stack Overflow" "The cat crept into the crypt, crapped, and crept out again."
SIRACARDFMVUICVSMORDZNAKECMZMFBCYNRDFMSVTVKBTMMY
$ node playfair "Lorem ipsum" "dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat."
CRORSDAHGAMQKPXDOFQMQAMSBSSPUPBPTDMOAHURNRCRLUAULRGNMLCPLSKDSBSBSQQAHMIGRERYMQCROREMAGDTSZIMUHAIAQRQALSGLAHSLZRQPIETAPDXRPNMSFRYMEBPZGHARKIEMIOGROIGREPUHSUPAQIMUHAPUOYRPGRLLRCRKPXDUYAINZ