Sonic Hurricane has put up a rather nice fundamentals video on waking up from a knockdown and your various defensive options while doing so. This is a good article for beginner to intermediate players. Check out the rest here. Here's a sample:
If there’s one thing we’ve learned about the SF4 generation through two years, it’s that they love their wakeup uppercuts. The goal of this article is simple: to convince you to stop.
Think about who has the advantage in knockdown situations. The character on his feet can move around, establish his desired spacing freely, then attack at will. He can choose from his entire arsenal of moves, because he can perform slow attacks such as overheads without worrying about being interrupted during startup. He even gets to decide whether to hover inside or outside throw range. Simply put, he single-handedly controls the initiative.
By contrast, the character on his back can’t move and can’t attack until a specific, predictable moment. The only advantage he has is that he remains invincible before that instant, which isn’t a real advantage because it’s only passive invincibility. As soon as it ends, he has to deal with whatever attack the opponent has prepared.