When I'm representing a seller, I always want to be present for the appraisal. I always bring along a package for the appraiser, to make the job a bit easier. In the package I have the site plan, a floor plan if available, a list of improvements the seller has made, a list of the properties I feel are comparable along with the reasons why, and a list of the properties I feel are NOT comparable and the reasons why. If I've been inside the comparables, or if a current photo doesn't represent the property when it was purchased, I document that.
Give input in the research phase; make the appraiser's job easier. You may come up with some comparable sales or insider information that the appraiser doesn't have. Now is the time to share information.
If you wait until the appraisal is finished, the odds of the appraiser changing the appraisal is nearly nill - even if the assumptions are illogical or incorrect.
Be PROactive, not REactive.

Wayne - thanks. Glad to know you do it, too.
Joan - I don't think giving our opinion on comps is going "over the line". The appraiser can take these or not, as he sees fit. Sometimes we have more inside knowledge about a neighborhood than the appraiser does.
Sharon,
You are so right on this one!
I can't begin to tell you (or actually you do know) how often the listing agent doesn't bother to show up, maybe an assistant at best. Why on earth would you want to make this process difficult? Somehow some are clueless to the value of time spent here. And I love telling my sellers that it's my normal practice to meet the appraiser when it comes to their home.
Hopefully newbie agents will understand the significance of your post. BTW, I completely agree with your response to going "over the line".
Sharon,
I try to do the same thing but sometimes i have seen them want us to to let them do their job by themselves...I always offer floor plans and comps. I do let them go about the business so they can get the appraisal done as quick as they can without interruptions but I do lend my ear if they need assistance.