I've never met someone who hasn't liked the AudioEngines, and apparently they pack penty of bass wallop on their own.

also, be sure to visit audiostream.com where Michael Lavorgna reviews a bunch of desktop systems.

that would be acceptable? What will be your source? Budget?

I certainly wouldn't buy the Bose without listening to other options.

My first thoughts without knowing all your requirements:

Emotiva mini-X a-100 amplifier $220

Totem Mite bookshelf speakers $725/pair

Hsu STF-2 subwoofer $350

My wife insists on small speakers but wants great sound.  I have demo'd dozens of bookshelf speakers, listened to the BOSE system and what I am lisiting below  are the smallest, great sounding speakers I have been able to find.  These are all Home Theatre lines but they all do a great job with audio as well. 

Sunfire HRS SATs are 5.5" x 8".  The sub that matches that line, the HRS8 is a 10" cube.  This is an audio sub, it is not a home theatre sub.  It is very refined, lots of detail and not boomy.  If you want booming bass, this is not for you despite the fact it is 1000w.  I own the HRS's and they are in a 7.1 system but I reguarly listen to audio in 2.1 and am extremely pleased with the quality. 

Sunfire makes a nicer speaker called the CRM-2 that is a touch larger at 8.25" high.  It is a great sounding ribbon speaker.  Very warm, very detailed.  You could match it with that same HRS sub.  When I demo'd these I wished I could afford them over the HRS's but couldn't do it in 7.1. 

The only issue with Sunfires is that they are extremely inneficient and require a lot of power to generate volume.  The HRSs list at $900 a pair and the CRM-2 list at $1600 or $1700 a pair. 

For something a little less expensive, B&W H-1s' are great sounding for the money.  I have these in a 2.1 system in my living room.  They are 4.5" x 9.8", priced at $500 a pair, are easily wall mounted and can be turned horizontally if height is a bigger issue that width. They are much more efficient than the Sunfires.  The sound is not as detailed as the Sunfires, but the price is not as high. 

Other options: 

Polk makes this Blackstone series that sounds good, not great.  I have the model line that preceeded Blackstone.  Detail is good but not in the same class as the B&Ws or the Sunfires and are only nominally smaller than the others.  Also, compared the the B&Ws and the Sunfires, I find the Polks to be bright but they are only like $300 a pair.  Def Tech has a satelite that also sounds good, not great.  Maybe a little less bright than the Polks but $400 a pair.  They are similar in size. 

If you need something smaller than these, computer speakers might be the way to go.