Silver was my preference of the originals, it was the second ever game I owned/played after yellow and it turned out my best friend (who had gotten me into the games) had chosen Gold. We pretty much beat them together, trading to help each other out, mystery gift and we even both beat the elite four sitting right next to each other at a sleepover.
I had even traded all my Yellow bests over to it including mewtwo, the legendary birds and my first ever caught pokemon, a pigeot called Windy. I ended up reaching 17 elite four defeats and 3 level 100's including Windy. I remember catching Lugia with a single greatball on my trainer. I hadn't realized that until I found it and since it was such a ***** getting through the whirl islands I said 'screw it, I'll just keep resetting until the damn great ball works' but all be damned it worked the first time.
It still bums me out to think how it's all gone now. It died in around 07. I had just barely found out they could die as my gold had the previous year.
So out of nastalgic biased I prefer Soul Silver and Windy now has a son, Windy II.
Once I get a job I'll probably end up buying Heart Gold though. I personally don't think the exclusives make a big difference and the cover legendaries are in BOTH versions.