I'm going to convert a lot of flacs to oggs for listening on my karma. I'm planning to encode at 5.0.

This quality is fine for me.

1) Should I still be using the gt compile?

2) What's the difference between using 4.99 and autov? Anything noticeable in size or quality?

So, here's #3 - what do I do?

[sorry for not getting the names complete and correct - it's not on the tip of my tongue]

for #1 use whatever sounds best.
for #2 4.99 autov sounds good to me and has a bitrate of 140-150k
for #3 Just panic

I use aotuvb2 -q4 for my Karma. I've never had a problem with it. I'd suggest, as the previous post suggests, you find what works best for you and your portable situation. I used to have gt3 -q6 on my Karma and then I realized that I couldn't tell the difference between a -q4 and the original. Saves space and I realized that infloated bitrates aren't justified until you actually test them.