3.1 or 2.1 Home Theater setup for desktop

If you really want a center channel, probably the easiest way to do this is get one of the higher end multi-channel sound cards, such as one of these:

Asus STRIX RAID DLX
Creative Sound Blaster Z
Creative Sound Blaster Live! 5.1
etc.

Then you'd have to find 3 channels of tube amp and 3 speakers, plus a power sub.  The 3 channel solution is a lot more complicated.  Of course, you can get a 5.1 channel computer speaker system.  Logitech offers several options.

The 2 channel route will get you better sound quality.  You can start with a high end 2-channel sound card such as Asus Xonar Essence STX II or EVGA NU.   Or you can look for an external USB DAC.  You'd have to get a power sub and then look for either powered monitor speakers or speakers+amp.

$1,000 is not going to get you very far here, unless you go on the cheap.

The problem with Sonos is that it only has HDMI/optical inputs.  No USB input.  Plus, if you really want a sub, $599 will get you a rocking Rythmic sub which is going to be a lot better than the Sonos for the same price.

I would do this in stages. Look for a USB DAC with a volume control.  These are a couple that are not too expensive (for what they are), but are about half your budget.  You can get them for less used on ebay or other sites:

Parasound ZDac
Cambridge Audio Dacmagic Plus

Both of these or USB DACS and have both XLR and RCA outputs that can be used at the same time.  Look for some nice powered monitor speakers.  Think Yamaha HS5 or other powered monitors.  You can add a powered subwoofer of your choice at any time in the future using the second set of outputs from the DAC.

Alternative, you could go for that tube amp and look for some nice bookshelves (Elac is the only one that comes to mind that is cheap enough but still very good).

@lalitk - "thatcdac" stated that these would be used on a desk and titled his post "desktop".  In a later post he somewhat confirmed his position on computer because he does not want to use an internal sound card on his computer because of technical reasons.  This leaves only the option of a USB DAC with a volume control.  I do not see anywhere that says this is a normal TV/entertainment setup.

@thatcdac - I agree that tube amp is not really recommended here.  You could go that direction, but the budget is going to be more like $1500, and that does not include a subwoofer.  Also, tube amps are going to be low power and tubes will start to saturate once they get past half of their power rating.

I'll repeat my initial DAC suggestions here (they are in the $500-600 retail area, but can be found for less used):

Parasound ZDac
Cambridge Audio Dacmagic Plus

The Parasound ZDac has a better stock power supply (internal linear power supply), but ZDac can only support audio files up to 24/96 resolution on the USB input (24/192 is not supported).

Cambridge Dacmagic Plus will support the higher 24/192, but comes with an external switching power supply adapter.  So the stock sound quality will not be as good as ZDac, but you can always upgrade this to something like a Teradak linear power supply (another $200-300).

For speakers, the easiest solution is to get powered monitors (speakers that have the amplifier built in).  My own personal recommendation is the Yamaha HS5, which retail for $400 a pair.  You can look at others if you want.  Then just get a couple of XLR cables and connect the DAC directly to these speaker - and you're done. 

Cost for this solution is about $1,000 (or just under).

Alternative, you could do a set of normal speakers and an amplifier here, but the budget is likely to go over $1,000 (probably something like $1200-1400).  Low cost amps are stuff like Parasound Zamp ($350) or Emotiva BasX-300 ($399).  Plus speakers.  A low cost bookshelf speaker that still sounds very good would be something like Elac Debut 2.0 B6.2 at $349).

These are just different ideas on approach.  With these two DACs, you can always add a subwoofer to the system later on at any time.  A really nice reference subwoofer for the money is Rythmik Audio L12 for $559.  It's not really huge compared to other subs (14" x14" x 15.5"), but Rythmik is one for sound quality.  There are smaller subs you can get and also cheaper subs.