The first one I owned was Yellow, but I had played a lot of Blue as my friend had it on his gameboy (before I had mine, I saved up and bought one specifically for Pokemon XD).
But I got Silver pretty much on release, and I'd say that is was my favourite experience of the lot as it was an entirely new adventure, with new Pokemon, that I got to experience in its entirety from the beginning! As others have said, the day and night system (I never understood how it worked, it never occurred to me there might be a battery in the cartridge itself lol), breeding and the two regions really added to the game imo.
That said, I got Pearl when I first went to uni, and three of my flatmates also had either Pearl or Diamond, and it was an absolute blast racing each other to the Elite Four and then battling our teams against one another - very good memories!
Last year, I picked up Omega Ruby, and again (even though I didn't have anyone to play it with) had it was just as good as ever, so am waiting for Sun/Moon to come out to start all over again .