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Two professional letters of recommendation?

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I'm in a bit of a bind at the moment when it comes to getting 3 letters of recommendation for applying to a computer science PhD program. I graduated from college about 4 years ago and have been working as software developer since. I haven't managed to do any kind of academic work lately so I don't have any professors that I've been in contact with recently. I decided that I've waited long enough and that I should just go for it. So, I'm planning to apply by Dec. 15th this year with whatever I can come up with.

Right now, I have one professor from my undergrad days who still remembers me well and has said that he can and is willing to write a strong recommendation for me.

The other reference I have is one of my current managers, the VP of Technology of the company I currently work for. This isn't a research-oriented reference, but I'm hoping that the development lead roles I've taken will be of some help for my application.

For my third reference, I have three choices. I could ask a former manager for a recommendation. I'm sure that she would be willing to write the best recommendation she can, but compared to my current job, I had more of a junior position when I worked for her. I could ask another manager from my current company to write a recommendation. I have a feeling that that wouldn't be of much use though. My last possibility is to email every professor I've taken a class with and had gotten a good grade from. The problem with this is that there's no other professor (other than the one who agreed to write me a rec) whom I've taken more than one class with. I'm sure that none of them remember me and even I barely remember what I did in any of those classes.

What's my best choice if I had to pick one of them?

If I end up with two strong recommendations, and one that's clearly lackluster, what are my chances of getting into some kind of decent program (I.E. one that I can effectively do research in, regardless of where it's ranked)? My GPA is 3.49. I have yet to take the GRE. When I took the GRE four years ago, I sort of just walked in without doing any kind of preparation at all. The score I got was 580v,750m,4.0a

Thanks for any advice.

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