The Z-5500 has a bigger subwoofer, its 10" vs 8". For Logitech tho, bigger might not be better...I might prefer to pay $100 NOT to have the bigger, boomier sub 😛
Also, I believe the Z-5500s fixed the problem of significant satellite hiss...that was the main thing holding down the Z-680s, in fact you could say the Z-680s were a faulty product. I've had them for years and I spent more times listening to my headphones than the Z-680s. The hiss is very loud, its about 30-40db which is in the range a CPU fan. running at 1,500rpm.
If I had to get a Logitech, I'd say the $100 was worth it, just for the hiss issue (it's very pervalent). However, I don't think I'd ever drop only $200-250 and hope to get a decent 5.1 setup. I think anything below $500 you won't get a system that satisfactory in both music and gaming... Something like a Creative S750 or a Fluance HT set with an AV receiver is on my my mind )