Sounds okay to me if you are using your laptop as the source cos if you are playing MP3s, there is never sufficient encoding in MP3s to do justice to the music anyway. However, it is a first step towards REAL hifi (and getting poisoned) as PC speakers are shit. Subwoofer is great if you are a bass-head like a few of us here as it gives practically everything a good thump. Never heard the Yamaha YST-Sw90 before as I myself have an old Japan made BMB subwoofer (nowadays BMB are made in China) but I did audition the SONOS subwoofer over the weekend at Harvey Norman and the bass actually sounded strong and tight. Didn't check out the price cos my missus was eyeing me from afar and I could feel the piercing stares and I wasn't hunting for another sub anyway. Yamaha receivers are good (especially when it has a dedicated sub out) but you will need to look for a subwoofer cable to connect these two together (another hit on your budget). As for speakers, I personally prefer Dynaudio and if you are playing MP3s, use a 14 gauge wire for your speakers as I don't think it really matters. Save on the speaker wires until you get a dedicated CD player as your source. For the 14 gauge speaker wires, you can get them at Radioshack.

3k budget.....

here's my thoughts:

amp: go for a used amp....something like Audiolabs 8000A MK2....should set you back around 1k

speaker: agree with XLS Encore

i'd ditch the subs and go for a proper speaker stands

speaker cable....if no budget, strip the network cable and use it first....
little budget....you can try Canare, Belden and plenty more.....you can search for Black Octagon...he does a number of DIY cables at affordable price

hardware is just the start....having the right setup and tuning is second part.....and more to come

i'd suggest you start with this kind of setup and slowly work your way into it