According to the description of the homepage of Proxifier, the software Privoxy looks like a good recommendation. Privoxy is a proxy application which filters a lot privacy related things (cookies, webbugs etc.). However the software allows you to configure HTTP, SOCKS and other types of software and is very flexible. I am sure that this is a good replacement.

After reading your comment I can go a bit more into detail:
The central configuration file is /etc/privoxy/config. The directory /etc/privoxy has some other files, too. The config file is very well documented.

Lets assume you want to send all traffic to example.com though proxy-a and all traffic to askubuntu.com through proxy-b. SSL/TLS traffic (HTTPS) should not use any proxy. So you add the following lines:

forward .example.com proxy-a

forward .askubuntu.com proxy-b

forward :443 .

The keyword forward is followed by a site or a pattern. It can be an IP address, hostname or a regular expression. All traffic which matches will be send to the last entry in the line. This the proxy address. When you use a . (a dot) a the end of a line, it means that the pattern before will not use any proxy. You will find more information at the handbook.