The antenna is the broadcaster to the outside world. If it has the correct design and implementation, you will get out exactly the signal you want at exactly the right size. There are thick books dedicated to the design and creation of RF antennas. Suffice it to say that a base-level knowledge should be good for what you are likely to deploy. There is a critical trap to look out for however: most readers ship with one or maybe two types of antennas. The antennas shipped with a reader are not always the best ones for your particular application.
As you become more familiar with readers, antennas, and RFID deployments, you will start to form a picture in your mind of what an antenna "lobe" looks like, even though you cannot see the radiation pattern coming from the antenna. A UHF antenna has two types: linearly polarized and circularly polarized. The linearly polarized is highly concentrated and highly orientation sensitive. You can think of it as a slice of RF that is very vertically focused, like the type of light that might seep in through two slats of a window blind. Because of this narrow RF lobe, the tags have to be in just the right orientation to be read. Linearly polarized antennas are highly sensitive to the direction and orientation of the tags they are reading, but they provide a more-concentrated RF signal and therefore can read tags at a greater distance than circularly polarized. Circularly polarized antennas send a vortex of RF in either the clockwise or counterclockwise direction, and the lobe usually looks like an inverted pear or apple propagating from the antenna. Circularly polarized are a lot less susceptible to orientation and cover a wider area.
HF antennas are the other type of antenna you are likely to work with. They require that the tag be coupled with the antenna and therefore read at a much closer range. They are also much easier to make and tune, because the typical HF antenna is just a whole bunch of wire looped around again and again and tuned to the proper frequency (13.56 MHz). The loop antenna can be designed, therefore, in many shapes and sizes depending on the application.
The last part that you need to know about antennas is the installation. Many companies make specialized RFID racks. Symbol Technologies and Alien Technology have racks that fit their readers and antennas, although they do not have much control and flexibility in moving antennas and adding peripheral devices such as UPS systems.
At ODIN Technologies we make a rack that works with any reader or antenna combination and allows antenna shaping and tuning. There are also many custom shops that, although more expensive, can create a rack specifically to your needs.