I'll give my thoughts. Note that while I agree with lane_miller that hearing a band's influence is a factor, really, whether we like it or not (for most prog fans, not), number of albums sold is a factor. I'm probably leaving some out, but these seem to me to be the most influential of each decade (note I'm also counting each band for the decade they began in, not the decade they are most influential during):
In no particular order for each decade:
70's:
Yes
ELP
Pink Floyd
Jethro Tull
Kansas
King Crimson
Rush
Frank Zappa
80's:
Dream Theater
Fates Warning
Queensryche
Savatage
90's:
Pain of Salvation
Symphony X
Flower Kings
2000's:
Redemption
Riverside
Pagan's Mind? (though they straddle the fence between prog and power, they seem to be influential)
It's really tough to say who's influential after 2000 though, I think.