Let me put in a shameless plug for t-amps here. As long as you can deal with their limitations (usually limited to 2 channels, and wattage before distortion is limited), they sound great, they're very compact, and they're extremely energy efficient. I did run my bookshelf/sub setup with an Onkyo 7.1 receiver at one point, but it just wasn't adding anything. Actually, it was noticeably hurting sound quality/clarity, partially because it insists on processing the audio for surround (don't do that, just amplify the darn input and send it to the output, each channel separately). I sure don't notice any clipping with the t-amps either, particularly at any reasonable volume (granted, small to medium size room at home).
My setup with the Pioneer BS22's and acoustic audio sub entails the speakers being at the far edges of the desk (8' in an 11' room), the sub being off to the side, the little amp on my monitor stand (it fits easily), and half a spool of speaker wire to make it work. Sound is clear, it does the job nicely, and bass is only obnoxious if I set it to be.
Little disclaimer: This usually requires you to run the line-level signal through the sub. BE CAREFUL - t-amps tend to use floating grounds, and can fry if you connect them (they're usually not connected for that, only +/- shorts). My particular sub happens to isolate the grounds, so this is fine, but not all cheap ones do.