I use Stamp. It's awesome.
I use it to download the files right off the card. You specify the destination folder. If it doesn't exist, it'll create the folder for you. You specify exactly how it is named. For example, I name my files by time and then image number... so a file IMG_8763.JPG taken at 3:45:23 becomes 154523_8763.jpg. This way there is almost NO chance of overlapping file names. In the case that there is, Stamp is smart enough to add a serial number to the end so it won't overwrite.
Then import the set into lightroom and you can cull from there, or pre cull using something like pixort and then import. Because the filename is the time, you can sort by filename in lightroom. This comes in really handy when you start stacking files and creating TIFF or PSD files, because by default, it sorts by import time so it puts all your CS2/CS3 edited files to the end of the list, which sucks.
You can get Stamp here: http://www.snapfiles.com/get/stamp.html
best part is that it is FREEWARE! If you try it out and want help setting it up, let me know. I'd be happy to help.