I use CuteFTP and have found NO problem in uploading larger websites. I tried the Professional version for a short time and never used all the options, so I bought the Home version. Two of the sites I maintain are over 2500 files.
I'd reccomend SMART FTP to, sturdy software that can upload good amounts of data. Although from my experience when uploading around 500mb of data I've had the software stop uploading on numerous occassions so be wary of that. Apart from that its simple, easy, free software that I would say is wicked....
I use Cyberduck, but this is only because I'm using a Mac. Before I used FileZilla which worked most of the time, until recently when it bust up. That was really annoying - Cyberduck for me
After trying many FREE FTP software, now I use Filezilla because it
enables FTP connection through a Proxy. Another feature I like is the
ability to delete folders recursively. This was a feature missing in the
FTP software which I used earlier, and deleting folders with a deep
structure was a troublesome process.
I use CoreFTP lite. So far I have had no troubles with it. It's very easy to use. The interface isn't so pretty but It's functionality makes up for that.
I use FireFTP for whenever I am just browsing and want to check something, it's good for stuff like that because it just opens as a Firefox Tab. But for normal FTP'ing I use either Smart/Cute depending on which computer I am on.
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