I downloaded MP3Gain to adjust the volume of my MP3 collection, but I don't know how to do the same with my APE collection. I'd like to do the same also with other formats like MPC or OGG, I know it's possible but I don't know how to do it...Please help...

Please check the wiki/Knowledgebase Project before posting:

http://doc.hydrogenaudio.org/wikis/hydrogenaudio/ReplayGain

I tried to use the latest version of Foobar2000 with my APE collection and it works but I think it uses the standard value of replaygain (89 db) for the operation; is it possible to set a different value for the normalization?

You can adjust it in the playback settings.

Thank you very much!