Crimson Dark is a pretty good one, though it takes until the second chapter to really hit its stride.
http://www.davidcsimon.com/crimsondark/index.php?view=comic&strip_id=1
I see the Awesomeness.
Schlock Mercenary. Epic commitment to updates. Ten years of updates everyday of the week.
Fight smart, not fair.
DUMB
We have Notable Sci Fi Webcomics.
I'll second Schlock Mercenary and bring up A Miracle Of Science, which is completed, and its sequel Afterlife Blues, which is not, and which I really need to get around writing a page on.
[1] This facsimile operated in part by synAC.
Zzzzzzzzzz
Define "good" and "sci-fi", please.
...if you don’t love you’re dead, and if you do, they’ll kill you for it.
I'm watching you. ಠ_ಠ
Terra found @ http://www.terra-comic.com/ is pretty good.
Edit: fixed 
edited 5th Nov '10 8:25:27 PM by LanceManley
Education without values, as useful as it is, seems rather to make man a more clever devil. ~ C. S. Lewis
Not Actually Indie
That link is broken for me.
I've got a few on my favorites list that I've enjoyed, but it would help to know what your criteria for a sci fi story were beyond "good."
...eventually, we will reach a maximum entropy state where nobody has their own socks or underwear, or knows who to ask to get them back.
I see the Awesomeness.
He left a close parenthesis on the link. Cut it off and the link works fine.
Fight smart, not fair.
AXTE INCAL AXTUCE MUN
Freefall.
Nitz the Bloody
Well, you could do a lot worse than check out my own webcomic. Especially since this part of the story is building up to the big finale'...
www.rubysworldcomic.com
We Are The Wyrecats Needs Tropes!
Seconding Freefall. It's the most sciency out of the sci fi webcomics I read.
Starslip is a good sci fi webcomic too but it focuses more on art and the museam (haven't read it for a while so it may have changed).
edited 7th Nov '10 1:48:50 PM by Gvzbgul
Anyone know of one with decent art and a regular update schedule?
My other signature is a Gundam.