Shift clicking doesn't apply at all?
If these programs give you guys trouble due to the fact that you only want to use or sync part of your collecton, then you might think about doing what I do. I don't let anything on my Pods unless the tags are perfect, but i haven't yet tagged everything nor will I ever. What I do is split my music directory in two with "sorted" and "unsorted" sides.
WMP, Xplay, iTunes, whatever, all deal with the sorted section only. I yet to see a utility that did not let you define where the syncronization comes from.
Also, even though I've now dropped it, Xplay can be used to drag and drop files to your iPod any damn way you want: Explorer, WMP(10 is broken right now), even the Send-To function. I put a link to Xplay's iPod directory in my Send-To folder and then I can just right click on a file, group of files, or folder and have it sent right on in. Xplay, isn't free, but if you know how to use it, it's pretty slick.