Well, I admit I went ahead and googled FLAC and APE cause I had no sweet clue what either was, and the last two posts confused me. FLAC in simple English on wikipedia ftw
Anyways, that said I prefer to listen to cds on a stereo. I still download some albums, but not as often as I used to and I much prefer listening to cds on a stereo instead. I'm not any kind sound techie or anything so really all I can say is that what I rip to my computer/MP3s in general don't usually sound as "full" to me.
I'm not sure how what you've described has affected albums being labeled as "classics" in the 2000s. The only way the rise of MP3s may have affected that is that it's harder (at least for me) to appreciate something I only have on MP3 as a classic. I can still do it, but I like to have the whole thing in front of me. Maybe people have come to appreciate music less because it's become more accessible. I don't know.
The other thing, too, is that the 2000s really haven't been a huge era of breaking boundaries in extremity as of yet (which, personally, doesn't bother me too much. There's already so much to discover from the 80's and 90's anyways). The majority of the 20th century saw the rise of countless genres and sub-genres throughout music, and the 2000s don't have that kind of history. That said, I can think of a few albums that I would call classics from the last decade, though. But I don't think any band has really waltzed in and ripped the metal community a new asshole like was done repeatedly in the 80s and early 90s. Doesn't mean there haven't been some great and even classic albums that have shown that you don't need to reinvent the wheel in order to write a timeless album.
As far as how the music makes me feel. I definitely enjoy the music more in a cd, cassette or vinyl format. If we put it all on a scale, with a concert being one of the best ways to experience music and get that adrenalin rush from it, or just appreciate the music, then I'd say MP3s are all the way on the other side for me. It's hard to get as good a grasp of the album, it's musicianship an atmosphere just by MP3. At least for me anyway, but then I do really enjoy having a physical format in front of me so that might affect my view.
That might not have completely answered the OP, but I'm a bit clueless when it comes to that sort of thing.