Multiple connections in a single window
The one main thing which actually annoys me about flash is the fact that in order to connect to a large number of servers I have to open a large number of instances of the program, which uses memory AND (even worse) taskbar space. I've been using smartftp lately, and I love the way they manage ftp sessions with a bar listing servers. I also like the way they have a global queue setting so you can queue transfers from multiple servers and then have it go through in order while you sleep instead of having to simultaneously download from all of the servers at once.
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