You need to connect to a MS SQL server from Linux from the command line and you don't like isql. The solution may be FreeTDS + sqsh.

Setting up FreeTDS

In sid you can choose to use freetds-dev or tdsodbc. I choose the later. On sarge you just have freetds-dev.

Now you just have to edit /etc/freetds/freetds.conf.
The most simple configuration could be to add at the end of the file:

If you've multiple SQL server instances on the same host you may have to change the port (faster "handshaking") or compile the instance field.
You can find a more complete list of options at: The freetds.conf file

If you need to connect to a MS SQL server through PHP (or other scripting languages) you may consider the sybase libraries and set of functions. For PHP the packages are called php4-sybase and php5-sybase and will let you use the sybase_* class of functions.
In Debian sid and sarge you need to recompile PHP in order to get access to the mssql_* set of functions. I don't know if it is worth.
Another option is to use ODBC.

sqsh

Well you just have to install sqsh but be warned that in Debian sqsh comes with some annoying dependencies (libx11-6, libxext6, libxt6).
Docs for sqsh can be found unsurprisingly at http://www.sqsh.org/.