Fortunately, it's very easy to upgrade the firmware via tftp, http or https. All you need is access to a tftp, http or https server.
To upgrade the firmware without using a Windows PC:
http://your.spa3000.ip.address/upgrade?urlwhere url is the url of the location of your new firmware file, e.g. http://kirriwa.net/john/doc/spa3000-03-01-10-GW-d.bin This is Sipura's firmware version 3.1.10d - feel free to use this URL to download the firmware.
Note: I've read reports that echo is worse with v3.x firmware than with v2.x. I didn't run v2.x for very long - I had problems with incoming caller ID with v2.0.13g, which were fixed in v3.1.10d, and I didn't try to solve my echo problems until after I upgraded, so I can't say whether v2.x was any better. I don't use the SPA-3000 any more; I first replaced it with an Open 812L, but now I have an IP04 runnning Asterisk.