I know this is the third rail of Cycling, but since it's also the single most vital issue to the sport's health, we have to wonder... was this Tour a "clean Tour"? I'm saying yes, so far.
First, the definition of "clean" can't be 100% pure as the driven snow; it refers to the essential competition being untainted by drugs. This refers to the main protagonists being clean, as well as the larger forces driving the peloton. I'd say you need about 90% or so of the workers being clean too, so the average daily pace isn't affected. Also, "so far" refers to what we now know. In 2006 the LNDD broke the Landis positive within 48 hours, but I wouldn't rule out the chance that they're still doing tests, given the go-it-alone structure of testing this year.
I'm something of a naif by nature, so react accordingly, but I didn't see anything that made me particularly suspicious. If you want to tag all surprise performaces as suspicious, you could wonder why Stef Schumacher won both time trials, or Bernhard Kohl found himself on the podium, but I'm not overly inclined to question them. Gerol run one of those "serious internal checks" programs, and it's not like these guys aren't strong, or that they sauntered away painlessly from the peloton.
We know who did dope, and when Ricco flew away from the group nobody could match his pace. Same for Piepoli (known) and Cobo (suspected). Everyone in the top ten suffered visibly at times. Sastre launched the only heroic escape on the Alpe, along with a lesser version at Prato Nevoso with Schleck and Kohl. Time trial scores were generally quite credible.
Perhaps the most interesting aspect of this Tour, though, is the significant role of team tactics. I wouldn't reflexively pronounce the Tour clean simply on the basis of CSC's masterful work, and teamwork wasn't exactly absent during the big doping era (most of which I sat out anyway and can't really speak of). But one thing we know about a doped peloton is that the top guys would robotically march up the biggest climbs, teammates or no. Among the many crimes against Cycling perpetrated by doping is how deadly dull the racing could be. Clean riders, by contrast, have limited matches to burn and dire consequences for running out. This calls for some pretty careful decisionmaking, and team tactics becomes ever more vital as a result.
I could be talked out of this, but my quick take is that things looked pretty OK to me.