Is a sub the main concern ? I think if you have the space go just like a living room, two towers slim for the front decent center and two book shelfs on either side of the bed on the wall then two subs budget subs either side of the bed or if your room has two front corners free then that'll be great. Slim towers won't give you much bass response but it's a step up from bookshelf on a stand or wall, Definitive Tech makes some slim towers, let me know your budget i could pull up a quick package list Think of a pioneer receiver something that you don't have to buy an additional dock, i have yamaha receiver its amazing but it's dock is ridiculously priced so a receiver like pioneer that can work with just plugging in your ipod cable or getting a $2 iPod Dock from ebay will work best for the price.
Edit: I can tell you from experience, that Dayton has some inexpensive very good subwoofers, you can get two of their 10" Subwoofers w/ 125 watt RMS amps in each i have a 250 watt polk sub and the dayton shakes my *** more. So I'd avise for them since their cheap you can put one in either corner for around $200 for both on eBay or if you look around i bought one of mine for $97, and one shakes amazingly imagine two, they are probably high enough for a night table
if your bed is low though i think you'll need to crazy glue your alarm clock down.
