Which tagging option would you suggest best for my MP3 files?

I am just using an iPod, sometimes iTunes but only to transfer files from my PC to an external hard drive where I keep my music library, while I use foobar to handle the rest.
I also have some lossy files, APE WV and FLAC.
I was thinking to start using APE + ID3v1, baring that all MP3 are currently in ID3v1 and ID3v2 so I will have to convert them.
I am asking this as from what I understand with the change I should eliminate the "squares" problem on iTunes; but I am wondering what tagging system will prevail in the future. Do not want to change (more or less 5000 files) and then change again.
Any suggestion?

Thanks in advance!
