DSFTP turns your DS into an FTP server. Connect to it with an FTP client on your computer and transfer away. Requires you to create some configuration files first, and transfers at about 30 kb/s tops.
DSLinux also has ftp, telnet, ssh, and SAMBA support so it can show up in Windows's "My Network Places" area. DSLinux tends to be faster at wifi transfers than most other DS homebrew, but still relatively slow, less than 100 KB/s.
I've also used HTTPexec in the past. I have it setup to connect to "http://MYURL.com/download.nds" and when I want to transfer a file over, I rename it to download.nds and upload it to my host. Not the best method, but it works for temprary transfers.