I have experience with desktop speaker systems but I am not a pro. Finicky yes. Pro no. Though I spend 70% of my listening time in front of my computer even though I have a very nice system in my living room.
I agree that NHT's Moo and Soo (M00 S00) is a highly regarded system. At the ~$1k it should be sweet sounding - though I have not had the pleasure myself. Other monitor type speakers from genelec, mackie, and JBL should be considered since they are all-in-one (amp and speaker). Just feed the source via RCA or XLR (analog sources only) and you have clean sound. the only thing missing is the preamp and the nicely finished speaker cabinets and grills.
My budget was not at the $1k mark for sound from my Apple G5 in my office. I opted for the Blue sky media desk [ http://www.abluesky.com/
] which is their entry level monitoring system. I would love to hear the Sky one system.
I have my Media Desk system connected to my apple G5, using iTunes with pure AIFF format source [the same system feeds my "main" audio system]. The relatively small 2.1 system is amazing for nearfield listening (seated at 2-4 ft.) the traditional bass-reflex monitors flank my Cinema Display with the subwoofer at about 5 feet away off of my right shoulder. Blue sky has a philosophy of crossing over their monitors at 110hz to the sub/amp unit, which (to me) is very appropriate for nearfield listening.
The sound is clear and revealing. I hear everything. Old Lightning Slim (blues) recordings are not masked in any way - the rawness is there. Through my very (very) eclectic tastes I have listened to many songs/recordings......And though not a musician, I can hear various types of mic-ing and guitar string types. Do I know the technical names of the strings? No. But they are clearly different. All this is presented by the Media Desks. Also because of this I have found out how poorly some recording truly are (sorry for the bad grammar). This makes sense since these monitors are intended for computer mixing set ups.
So my final suggestion is to consider powered studio monitor type speakers for your computer system. More truth, less flash. There is a wide range of options for all budgets. Note that the distribution of these speakers is different from typical home speakers - instrument dealers/musician supply stores.
I really enjoy listening to the music produced by my Media Desk's! Listening to The Shins currently, but listened to Renata Tebaldi and The Art of Noise earlier.
Let us know what you finally decide upon and why, it'll help others in the same position as yourself. Good luck.