Is getting a good grade enough to ask for a letter of recommendation for a grad school application? I'm about to start a 5th year Master's program in CS at my university (one extra year after B.S. for a M.S.). I've also been looking at applying to grad schools for a PhD program, and the main thing that I've been worried about is recommendation letters.

I know one professor somewhat well (took two classes with her, one of which was a project class where I presented to her) and I think she would be willing to write a rec letter. However, she's fairly well known in her field and I don't know if that makes it harder to get a rec from her.

But, most of the colleges I'm looking at for grad school need three letters. I've had good grades throughout my undergrad, mostly 3.9 and 4.0s. Because I was fairly comfortable with my classes, I rarely went to office hours. As a result, I don't think any of the professors who've taught me know anything about me other than that I was in their class and that I did well.

I'm totally unsure now about how to proceed. Is it normal for professors to be asked for rec letters by students they only maybe recognize? Do they usually say yes or no? What are my options?
The only guarantee is that if you don't ask, you don't get the letter. So ask. 

I'm sure your situation is common in large places and it is good to find ways to "stand out" with at least a few professors as you go along, but that is too late for you now if time is short. 

But ask in person, during office hours, and be prepared to remind the professor of your past association even if it is only a little. If you ask by email it is too easy to just say no, sorry. But if you get turned down in person you might also get some advice about how to proceed (along with the disappointment).