First of all, if you aren't currently riding much at all, then my main advice is just to buy something cheap and plan to replace it in 6 months. If you haven't ridden real road bikes much at all, they will all feel weird to you and you won't know how to tell if they fit, so you will most likely make a bad purchase. Try to buy something for $500 or so and don't sweat it too much and then replace it when you know better. When making this initial cheapo purchase, worry more about fit and less about materials or components or brand name. The most important thing is to get your body used to the feel of a proper road bike.
Secondly, you have to decide what you want this bike for. Most of the bikes in a bike shop will be "road bikes" that are targetted at racing. This is probably not what you want so you should ignore all these bikes. These bikes are usually very light, very stiff, very jittery, with tiny hard saddles, very low handlebars, no room for fenders or racks, with very aggressive geometry that requires you to be riding hard and leaning forward a lot. You probably want a bike to get around town, that's pretty fast, can handle some wet road, maybe a rack to carry things, that you could ride out on the weekend for exercise once in a while. In that case what you want is going to be a "commuter" or "touring" bike (note, NOT "hybrid" bikes or bikes with suspension). They should have a slightly more relaxed geometry, room and braze-on bolt holes for fenders/rack.
X. Saddle. The main issue here is that most "road" bikes come with saddles that are too small and hard for the way people will ride them. In particular, a correct saddle is a personal thing, they should be sized to your sit bones, you may or may not want a taint-saver cutout (I recommend them), and if you are not going to ride with padded shorts, then you should have a semi-soft saddle. (note : NOT one of those big honking "comfort" saddles, but a race saddle with small gel pads or something like that).
A really good bike shop will let you swap the saddle. Most won't. If you can't find a bike with a saddle you like, just replace it.
X. Stem / handlebars. This is one of the crucial fit adjustments. (I don't mention the seat post, because pretty much all bikes have enough seat post adjustability to fit any reasonable rider). Lots of stems now are the threadless kind without much range of adjustment. IMO that sucks really bad. It means that you need to spend more time in the purchase making sure that the stem/handlebars are in a good position for you. If possible buy something with the ability to do a little adjusting. In our modern era you probably won't be able to avoid having to buy stem extenders or a flippable step or something similar.
In particular, if the bike stem is already angled way up (as many bikes sold today are), then you won't have any ability to adjust up more. That means it should feel plenty high to you as it is. As you get more experienced you can buy another stem that's flatter to bring the bars down some. In addition to the bars moving up and down think about how you might want to move them forward to back.
X. Tires. People spend all this money on bikes and worry about what the frame's made out of blah blah blah which doesn't hardly affect your ride at all. The #1 biggest bang for your buck thing that affects your ride is tires. Most "road" bikes are sold with tires that are too thin and hard for what people use them for. Conversely, if you want a faster bike, you can get a huge bump by taking that old beater and just putting some thin hard tires on it. It's a lot like swapping snow tires for racing slicks on your car. There are basically two extremes (ignoring mountain bikes / cruisers / etc) :
Commuting / rough roads : you want something like 28c or 32c tire , with some real pattern on the tread so it can grip in sand and wet. Inflate to 60-100 PSI. The wider tire is a bit slower, but will grip a lot better when you go over rocks and sand and pot holes. The lower inflation smooths out road bumps and also provides better grip. (It's an old trick that in extremely bad grip scenarios you can deflate even more, but that slows you down a lot).
Speeding : on good roads, you can run a 23c tire at 120-140 PSI with slick or semi-slick tread. This gives you very low rolling resistance, you can just touch the pedals and the bike glides and feels like it will never stop. If your bike is in good kip, there should be almost no friction in the turning parts of the bike, it all comes from the tires on the road. Of course these tires are very dangerous in the wet or even on sand. The hard inflation also makes the ride very rough, and can make the bike feel "jittery" because every little pebble is transmitted to your hands.
Often people will test ride some racing bike and think "wow that's fast" when in really all they're feeling is properly inflated fast tires.
X. Some bikes I like :
These are all around $1000 sadly. Most of these are classified as "touring" or "cyclocross" now. In reality they're closer to old fashioned "road bikes" than the modern compact little racing bikes. An old road bike like a Raleigh or all the Japanese bikes had braze on holes for fenders, racks, had relaxed geometry for comfort on longer rides, had some more room for adjustment of the stem/handlebars, etc.
ADDENDUM : buying used can be a great deal, but you have to be pretty smart about the condition of the bike and pricing. Some people have very crazy ideas about what things are worth. They'll say "I bought it for $600 ten years ago, so I'm selling for $550" . Umm.. no. A used bike should be half or less the price of a new one generally. If you look around you should be able to get bikes like the above for under $500. Also, you should not buy anything very old. Even if it works great it will be a pain to maintain or upgrade because the components are not compatible with modern gear. The oldest you should go is early 90's , and you want Shimano kit (though the chance of getting Campy on a cheap bike is very slim, you don't want it because replacement parts are so much more expensive and hard to find). Some people have absolutely insane ideas about what very old bikes are worth.
For your first time buying a bike, you can get a decent approximation of your size just by taking your inseam * 2/3. So for example my inseam is 34" * 2/3 = 57 cm ; I actually ride a 58 or 59, but it's close. I don't recommend sizing yourself this way for a serious purchase, you should try the bike and feel it because bikes with different geometry can have nominally the same "size" ("size" = seat tube center-to-top length), but it's an okay way to size yourself to find a very cheap craigslist first bike.