Well, a lot depends on how one defines "clearance" -- whether it refers to one's "soft points" (tissues) or "hard points" (bony bits).., and where one happens to hit at the time!
My older road bikes all date from 1970 to 1989 and have horizontal top tubes that are parallel to the ground. On those, I try to always have an inch or more of ground clearance to my hard points (usually the pubic symphysis) with the tires I use most often on pavement. My soft points may brush the top tube with no real consequence when fully dismounted from the pedals on pavement.
My 2011 Sherpa has considerably more standover clearance, but it -- like many of the current crop of "compact frames" -- comes as a byproduct of other design parameters (i.e. a sloping top tube). Compact frames also have shorter tubing lengths, and thereby may be more rigid given identical tubing wall thickness and diameter (long tubes are ultimately more flexible, and shorter are less so, at least in the frames I've brazed from scratch to my own design).
All things being equal, it is nice to have a bit more crotch clearance on a bicycle that is used either off-road or on poorly-maintained roads. Nothing wakes one up quite so quickly in the morning as dismounting into a chuckhole and finding oneself "bottomed out" on the top tube!
Another thought, borne of experience -- having a bit of extra standover clearance allows for greater variation in tire profile/width (the two are closely related, often in a 1:1 ratio) and this allows for a bike with two quite distinct personalities -- one running narrow, low-profile tires for summer and wider, higher-profile tires for winter and foul-weather use. Depends on whether the rear brake cable runs atop the top tube as well; it does eat up another 5mm or so of clearance.
Best,
Dan.
