Unsubstantiated claims of "they all do it" are a big part of the problem with enforcing PED rules. Please refrain. Phelps, by all indications, is just a born freak. His body is horribly out of proportion to his legs, and freakishly large. Add proper training and well developed form you have what you have and no PEDs required.
The big item that Phelps has on his side (besides very obviously hitting the genetic lottery) is the history. It's not impossible that swimming's governing body is as hopelessly corrupt as the UCI was during the Armstrong era. It also seems unlikely that other member countries would be content to sit back and let the Americans go out and Hoover up medal after medal across the discipline unless they flat out couldn't catch them in the act.
The counterargument is that the Dana Torres renaissance looks uncomfortably like that of Roger Clemens, and that if she got away with it then God only knows what everyone else is doing.
The doping situation lacks easy answers. Should we cast a jaundiced eye upon a Dutch runner breaking an apparently unbreakable 400 record? How about Bolt and Michael Johnson's equally insane 200 record? Was Johnson clean? Bolt's 100 time this go-round was right around that of Ben Johnson in 1988, and he beat someone that got caught cheating in the process.
Can you go 9.58 without chemical help, the way Bolt did?
How would we have evaluated Bob Beamon's record after Calgary? Did Mike Powell have to cheat to get past it? Certainly, in his case it helps that Carl Lewis came close under the same conditions and that no one has even begun to come close since; it looks like what happened was a result of skill interacting with ideal (WR-legal) jumping conditions rather than skill interacting with the point of a needle. But most sports and records don't conveniently hand us that kind of data.
In the absence of a solution, I will say that I'll enjoy the kinds of sporting moments that can't be produced through PEDs - Federer's ability to find some absurd crossing angle that turns a lost point into a winner, Messi dribbling through a maze and then picking out a teammate with a perfectly weighted pass, or the metronomic skill of the Chinese divers. It's not that PEDs couldn't potentially improve the performance of said athletes by giving them just a split second more reach, speed or rotation, it's just that it can't possibly substitute for the grace and skill on display.