That's a very tough and generic question you just asked. Without specific details as to your listening material and usage of the system I can't get into specific brands for the audio. I will answer you in generalities based on my proffesional opinion and experiences.
Here's what I suggest...
Scrap the 50" or so plasma TV. In a room with that much space go with something like an Epson LCD projector. I just tried one out and think it's a fabulous product with a good price point. It's MSRP is at $1600. Get some Goo screen paint (which I am never a fan of, but you are on a budget and this will blow a plasma away) and paint an entire wall. I suggest doing the entire wall so that you don't have to build any sort of frame. This also looks cool if you paint the other 3 walls something dark and let the white/gray Goo wall serve as a sort of reverse accent wall. The color "Ink" (flat sheen) from Sherwin Williams is great for a theater and goes good with the white or gray. Total cost for the video is around $2200 MSRP but you will have a picture over twice the size of a 50" plasma with better picture quality for your movies. I also suggest the Epson because it's a dedicate theater projector, not some multimedia projector hacked up with a fancy case. It also has some really cool features like horizontal lens shift, so you can mount it right up on the ceiling. Epson make the LCD pannels for most LCD projectors out there and they have a two year full replacement warranty. I fully endorse their projectors over anything else in that market space.
For audio... at $3K you can't get too crazy. Would two subwoofers be better? Well, yeah, but your budget deosn't allow for two good ones. One good sub will have to do. Spend $550 on a good Marantz or Denon receiver, $250 on wire, and that leaves $2200 for speakers & DVD. Get the best matching set you can afford (I would not do inwalls since you are more than likely installing them on an outside wall). Bookshelves, not towers, will give you the best sound for your $ on your budget. Appropriate the most of the $2200 for speakers on the sub. I would spend $750 on the sub, $300 - $400 on in ceiling speakers, and the rest on the front three (remember DO NOT mix and match brands of model lines), DVD player, projector mount, and speaker stands. Wire for 7.2, but buy for 5.1 and see how you like it.
Note: Try to get a deal on all of the speakers and with the money saved buy an X-Box360 premium bundle ($400) for your DVD and you can add the HD-DVD attachment for $200 later (no, it won't do 1080p, but neither will your projector). I would also recommend getting a Harmony remote to controll everything.
PS... That budget is tough. I usually tell my customers that without $6,500 - $8K to invest in a system (not including the room) it's not a good idea for a dedicated theater. Most people want to be wowed when having a dedicated room like that and it's tough to do for under that (my opinion). Your budget is under $6K for video and audio I am assuming, but it can be done with a few compromises.
