Well, here goes. There really needs to be two lists: one list of the best pieces written for guitar and the other of the best pieces transcribed from other instruments and played on guitar. This is the case because a great deal of the best guitar repertoire is actually looted from other instruments. For example, probably the first two pieces on any list of great guitar pieces would be the Chaconne (from the D minor Partita for solo violin) by Bach and Asturias by Isaac Albéniz. Both of these are transcriptions.
Ok, so here you go, original pieces and transcriptions, five of each, not necessarily in order.
Top Ten Pieces for Guitar (transcribed and original)
1. Chaconne in D minor, J. S. Bach (transcribed from violin)
2. Asturias, Isaac Albéniz (transcribed from piano)
3. Twenty Variations and Fugue on "Folias de España", Manuel M. Ponce (original)
(Alas, there does not seem to be a really good complete version on YouTube)
4. Cordoba, Albéniz (transcribed from piano)
5. Nocturnal, op. 70, Benjamin Britten (original)
This is just the final passacaglia from the Nocturnal, but it is played by Julian Bream, who pretty much owns this piece.
6. Recuerdos de la Alhambra, Francisco Tárrega (original)
7. Concierto de Aranjuez, Joaquin Rodrigo (original)
8. Five Preludes, Heitor Villa-Lobos (original)
Unfortunately I have to run, so I will complete this list a bit later.
UPDATE: And now for the last two.
9. Sonata K. 213, Domenico Scarlatti (transcribed from harpsichord)
(This fantastic sonata by Scarlatti will have to represent all those great ones that many people have transcribed for guitar.)
10. Fantasia, John Dowland (transcribed from the lute)
(And this will have to represent all that great lute music that guitarists so often play.)