In our personal collection, as well as in our store, we have both new and "refurbished" instruments. Sometimes our customers ask us whether they should get a new "with warranty" guitar or one of our refurbished (never sold but no warranty) models. Our only piece of advice: don't let the warranty decide for you. Why?
First of all, if you buy a guitar from anyone who has a decent return policy, you have time to check for yourself if the guitar looks good, sounds good, and if the electronics work. And although the IDEA of a guitar warranty is comforting (you think "hey I'm protected if anything goes wrong"), in practice it's just not quite that useful.
Most new guitar warranties state that they will cover "defects in materials and workmanship", and for a limited period, electronics. The warranty is not without cost though, unless you happen to live close to a service center. You have to get it to and from their authorized service centers, and for a retail customer paying for shipping can easily cost $60 one-way.
(By way of contrast, should you have a problem, your local guitar repair shop can probably do a great job for less than the cost of shipping to and from the service center.)
In addition, if your guitar gets dried out and cracks, it's not covered. If your electronics fizzle after the warranty period (usually one year), it's not covered. If you sweat on your guitar and damage the finish, it's not covered.
So if you like the idea of having a brand-spanking-new guitar, get one...just make sure you read the warranty so you know what those extra dollars are getting you.