Wine works great for some software, but it's much better to use native Linux software where possible. For example, you say you are running a Windows version of SSH
under wine on Debian? Why on earth? Use the native SSH.
Also look at the octave
package. It is almost a drop-in replacement for Matlab.
There are lots of sites that list different kinds of free or open source software packages. Be sure to check out the Open Collector
which lists software for hardware design. You also might find something under Wikipedia's software portal