If you spend some time around here you'll notice many people are usually asking these sorts of questions AFTER they make their purchase. A wise man asks before.
When buying a home theater system you have many questions to ask yourself. I'll try to cover the major concerns.
1.) How many channels? There are many options here. You can go with a 2.1, 3.1, 5.1, 6.1 or 7.1 surround sound system. The ".1" means you have a subwoofer while the other digit indicated the number of satellite speakers. 2 and 3 channel surround is just simulated surround, not much better than a TV by itself, so I can't really recommend that route. In my opinion 6 and 7 channels are just too many. They would work great in a big room, but most TV rooms aren't that big. You can always expand on a 5.1, so that's the setup I recommend, especially for a beginner.
2.) HTIB or DIY? You have two options here. You can assemble all components yourself or you can buy everything bundled in a home theater in a box (HTIB). Generally speaking, HTIBs are inferior. This is because they usually lack in a wide variety of connection ports. Also, as you may have noticed, many are based on a DVD player. If you must buy an HTIB, make sure you buy one that is receiver-based so you have the flexibility to expand. (For good receiver-based systems, see Onkyo's HT-S series.)
3.) Connectivity? HDMI is the best cable out there right now, so you'll want to make sure you have a system that can handle HDMI. Also, make sure it's an HDMI switcher/repeater, not pass through. ("Pass through" means no processing is taking place.) In addition to at least two HDMI-in and one HDMI-out ports, you'll want at least one optical and digitial coax in, some composite connections, a few component video in connections, etc.
4.) Audio formats? Every decent product should have Dolby Digital 5.1 and DTS decoding capabilities. With the advent of Blu-ray a couple of new formats have emerged--Dolby TrueHD and DTS-HD Master Audio. These are uncompressed audio soundtracks that, given a decent set of speakers, will sound superior to the older formats, which are "lossy".
5,) Blu-ray? If you are planning on buying a Blu-ray player in the future you should "future proof" yourself by buying HD-ready home theater equipment today.
I have put together a budget HD product list for those just getting started: http://www.amazon.com/The-Best-Hi-Def-Home-Theater-on-a-Budget/lm/R1M8CM8FMVSKF5/ref=cm_lm_byauthor_title_full
If you feel too overwhelmed you can go with the Onkyo HTIB I mentioned earlier. The 6100 and above is HD.: http://www.us.onkyo.com/prod_class.cfm?class=Systems
Let me know if you have any questions. Good luck.