I was asked this question on a Dodger forum, and wanted to share my answer here.
How do I think Bonds will be remembered? I think better than most people are saying now. It also depends on whether or not he gets passed by A-Rod or anyone else any time soon.
The main reason is that the big number (career homers) is the most memorable number in sports. It's a number so important, that it wrongly transcends time... everyone who's been in MLB gets measured against that number regardless of the homer-friendliness of the era. (I should admit that I have predicted before that fans will start to gravitate towards era-adjusted numbers, which is kind of an argument against what I'm saying here.) If Barry's still #1 in 20 years, I expect that the natural inclinations of fans will return, which is number first, circumstances second.
In the long run, I don't see any reason why the steroid era will be viewed any differently than the dead ball era, or a live ball era, or any other pocket. Barry will always be a part of that, maybe even the first example, but he'll be tied to the era, not set apart the way it's happening now. People forget to hate assholes... look at how Ted Williams is revered today. (Ty Cobb is an exception because racism was a big part of it, and that's still a sensitive issue for the world, unfortunately.)
In fact, if the steroid era is viewed differently, I predict it will be even less anomalous. That is, it's entirely possible that performance enhancers are here to stay... that technology will always be one step ahead of Johnny Law, and in fact Bonds' transgressions will stand out even less, being reduced to an early adopter of a permanent change, rather than the King of a limited aberration.
I don't think this is a Giants fan talking, I think this is rational. How does it sound to you guys?