Who makes the best acoustic guitar?  

Firstly, you might consider stopping by a music store that carries a range of different accoustic guitars and with some sales assistance, try a few different makes and styles of guitars. This way you can find a guitar best suited to your needs before purchasing one online that may be a style of accoustic that you find difficult to play.
As far as brand names, consider an Ovation round back. It is a nice, light accoustic that fits comfortably against your body, is capable of beautiful sound quality and is an all around good quality guitar. Eric Clapton is among the noteworthy Ovation players.
Be sure to do a bit of testing before purchasing any guitar.

I have an Alvarez six string with electric hookup that puts out good sound. I also have a Fender acoustic. It's funny how both guitars sound differently and on some days the Alvarez sounds better and on others the Fender sounds better. It just depends on whatever mood I'm in. On the electric side I have a Fender stratocaster and a Peavy electric guitar. The Alvarez and two Fenders are both lefthanded guitars and the Peavy is a righthanded guitar that I merely restrung.
I always like the Epiphone roundbacks but could never find one lefthanded.
With me it was always... see what they have lefthanded and take what you get.
I want a Gibson lefty electric. I want to see how those sound.
In buying a guitar you factor sound quality, but most importantly it's about comfort and how the guitar feels on you.

It really depends on what you are looking for. Some people want a guitar with a smaller neck, others like wider necks. You might like a certain body type more than another body type. And even good guitar makers might have a bad guitar in there somewhere, so if you can, try playing the guitar first instead of just saying that since you know the brand is good, the guitar must be good.

That said, it does work to buy instruments online. I bought my guitar online and I really love it. It's a classical guitar though, so that wouldn't help you. If you've never looked at guitars before though, you might want to at least go somewhere first where you can try out different styles of guitars before you purchase one. I usually end up buying from the music store though if I take up too much of their time asking questions and trying out things, because I know how horrible it is to work a commission job only to have people ask you tons of questions and then never buy from you anyway.

I think Gibson's are the best! Martin's are real good also!
I think the best buys you are going to find, other than local, are on musiciansfriend.com! They have all brands on there, and they have good prices!

It really depends on what you're looking for. If you have some experience with guitars, try looking here.

www.projectguitar.com

Ebay or online is not the way to go. Taylor, Martin, Takamine, Guild, Ovation, Gibson are all well known brands. But there are countless other manufacturers that make equally great guitars for the same price. One of my favorites right now is Wechter.

Not to be bossy, but I think the way to do it is 1) go to the music store 2)play buttloads of guitars 3)decide which one you like 4)play every one of that model they have in the store 5) pick which one is the winner.

You might think the music store would hate me for all that trouble, but actually it's the opposite (i think, if not they hide it well). Nowadays, if I come in for a new strap or cord or picks they just give me the stuff. Maybe they're afraid I'll try all the picks out before choosing, hehehe. But I think it's because they appreciate my consistent business.

I have an Epiphone 12 string and an Epiphone 6 string guitar, and I love them both. For the price you can't beat the quality. The 6 string was only about $300, and it was well worth the money. Personally I like the feel of Epiphones and Gibsons, however everyone has their own style that they like.
I would suggest going to a guitar shop and trying out as many acoustics as you can, not paying attention to what brand they are or how much they are. Narrow it down to a few that you like and then narrow those down by your price range. You may find that you like a brand that most people either don't know of or as a majority don't care for. My advice would be to go for the one you like, despite the brand and what other people say, because you're the one playing it so it should be what you're comfortable with. However, some guitars are known to be cheap and break often so you should a sales associate at the guitar shop, they're usually more than happy to help.

A Fender would be a good choice.
About buying it on ebay - never buy a guitar there! As far as a guitar goes its better to play one yourself before you choose it. Spend a few days experimenting if you are serious about it and have the time!