What did Charlie's aunt do?

First of all, I'm pretty sure that's exactly what is implied, that his aunt abused him sexually. That is implied in the way Charlie gets the flashback of her rubbing his leg when Sam does the same to him. The situation is the same as it is motivated by the same feelings and not just out of mere friendship. This is only a slight hint, so it may be a bit confusing up until then. But it is later reinforced when Charlie is in the hospital and the doctor says:

Doctor: You said some things about her in your sleep.
Charlie: I don't care.
Doctor: If you want to get better, you have to.

And later it becomes pretty clear that there was something wrong with his aunt when he writes:

There were some very bad days and some unexpected beautiful days. The worst day was the time my doctor told my mom and dad what Aunt Helen did to me.

Now to the question why he still told Sam that his aunt was his favourite person. I think when he said that, he still believed that this is the very truth. Up until his actual suicide attempt after Sam shook up his memories, Charlie seemed to supress what his aunt did to him and was rather confused about his feelings for her. He only knew that he was a little boy and feeled a very strong emotional connection to his aunt, even if he doesn't completely know where this connection came from exactly or to which level it goes. I think at this point his aunt really still was his "favourite person".

It isn't until those strange memories about his aunt become clearer that he starts to realize the whole extent of his relationship to her and that this actually wasn't a good thing. And only then his love for her starts to change into maybe even wishing her dead. Though, I think even then he still is to a large degree confused about what to feel. He probably doesn't only feel guilty about her death (as she was about to fetch him his present when she died), but also about what he did (ingoring that he was only a victim to her) and also for maybe partly wishing her dead, knowing that it was wrong what she did but also not able to stop his feelings for her from one second to the other even though they're stained now. So he feels guilty for pretty much everything, what she did, what he did, that she died, that he maybe somehow wished her dead, that he should have wished her dead but couldn't and still can't, ... And this confusion and guilt is likely also the reason for his suicide attempt afterall. To say the least, his feelings are difficult at this moment.

As to his best friend killing himself, that isn't alluded to much and doesn't seem related to the matter of his aunt at all. It is another aspect of his troubled past, and maybe also an aspect to stress his own difficult mental state and the possible future he might have been looking toward.