SG1 used to be great...it's now ok to mediocore, on average, but still worth watching. Any show on that long is bound to go up and down quite a bit.
Atlantis...eh...it's ok. Babolyn5, I tried to watch and for me it's like Firefly, I found it either really dull or really annoying, or both, to watch.
I really haven't seen very many 'good' sci-fi series over the years...there just aren't that many made, compared to dramas or mystery or cop shows. Things like ST, SG1, and Galactica are rarities.