There is nothing more frustrating than trying to play, or listen, to a classical guitar out of tune. By design, a guitar can not be tuned "absolutely perfect" anyway, but here is the way I do it. (Note: fingers - numbers 1, 2, 3, 4; string numbers - numbers in brackets (1), (2), (3), (4), (5), (6); fret numbers - roman numerals I, II, III, etc.).
Lower priced, beginner, student instruments regularly have greater tonal errors than medium or professional guitars. Use an electronic tuner and be happy. The guitar should play well within the first five frets. If you don't own an electronic tuner, use a pitch fork to tune the first string (they regularly come at A-440 or V fret on (1) ). Tune the (6) string two octaves below the (1) string, then tune (5) string open to V on (6), then (4) open to V on (5), then (3) open to V on (4), then (2) open to IV on (3) and check (1) open to V on the (2) string. Don't change the tuning on (1)!! Instead, recheck (1) with your pitch fork and adjust the other five strings until they match with (1). Again, this guitar should play well within the first five frets.
Always, always, play your guitar at the proper pitch. A semitone too high or too low will change the performance of both the guitar and guitarist. Further, using Parkening's words: "It will drive those people with perfect pitch crazy". Transposing should be done musically or with a capo - never with the tuning.
For medium or professional instruments, use a tuner or the pitch fork method described earlier, then fine-tune this way: compare and adjust (6) open, in octaves, to 3 on VII on (5) and (1) open with 1 on V on (2). Then compare and adjust (6) open, in octaves, to 1 on VII on (5) with 3 on IX on (3). After, compare and adjust (5) open, in octaves with 1 on VII on (4) and 4 on X on (2). Notice that (2) is slightly sharp. Using this fine-tuning method, tune (2) slightly flat when tuning with (6) open "E", and slightly sharp when tuning with (5) open "A". Average it, or set (2) so that it is no more flat at "E" than sharp at "A". When tuned in this fashion, no one chord will sound more in tune than another.
When you check your tuning using a chord, avoid using thirds. The human ear doesn't hear thirds as accurately as we hear ones and fives. EG: "A" chord - (6) open, (5) open, (4) 1 on II "E", (3) 1 on II "A", (2) 4 on V "E", (1) 4 on V "A".
It takes a long time to develop an "ear" to tune a guitar - it's a practiced thing; work at it and it will become easy. Until then, get a guitarist friend to help or use an electronic tuner, and most of all - have fun!- Ben Tobiasson