A lot of pc speakers use the enclosure as a means of generating deeper bass sounds - simular to how a guitar uses its insides to amplify its sounds.
The amount of air in the enclosure is important... as they usually use a bass port. The port is a hole that is 'tuned' to produce a low bass note sound when air blast through it.
If theres too much space in the enclosure - or no enclosure at all... the bass port wont function correctly. If there isnt enough space... the depth of the sounds will be minimal and possibly distorted.
The sides of the enclosure also act as a voicebox... and reverberate when the sounds blast against the walls... simularly to the bass port - same rules apply.
Anyway... just keep the rear enclosure to keep the bass... or, make a custom enclosure by mocking it up with oversized wood - and making more or less room in it by moving the wood pieces closer or further appart.. and once you find the correct volume of air... then mark the cutlines off and build the thing.
Im not a speaker expert... and may have described some of the things incorrectly.. but i have made a nice elclosure recently using the above method and it worked out fantastically.
Ohh.. and i think the padding stuff used on some spearkers is just to keep the thing from rattling. If it were for enhancing thud.. the speakers would have to really crank some major power to compress that stuff enough to do that - so its highly unlikly it would be usefull for small pc type speakers.
Also, if you want some rocking bass... I HIGHLY suggest grabbing some 'bass shakers'. They are like subwoofers... but do not move air arround and do not require a lot of power... yet produce incredible bass 'vibrations' up to 30 pounds per foot! (imagine someone slamming 30lbs into your back. They really can hit hard : )
I can hardly describe how much cooler these are than typical subwoofers. Youll get more vibration, with tons less volume... whereas you would usually have to kill the neighbors to get the kind of vibrations and impact made with the sub as youd get with these little things.
www.partsexpress.com has them on sale as a closeout. I had gotten a set of the 25 watters on ebay once... and they are strong. Though p.express also sells the pro ones that handle 50watts... which must be sick powerfull : )