Still Available
Disclaimer: I have no experience with these firms.
Video 61 & Atari Sales of Stacy, MN lists the following on their website:
$19.95 BATLE OF ANTIETAM [sic]
$29.95 GETTYSBURG THE TURNING POINT
$14.95 NAM
$19.95 PANZER GENADIER [sic]
$19.95 REBEL CHARGE AT CHICKAMAUGA
$19.95 SHILOH GRANTS TRAIL IN THE WEST
Old Software.com lists the following on their website:
Commodore 64:
Wargame Construction Set (SSI) 1987 Consumer Electronics Showcase Award Winner. Design your own war games for the Commodore 64. New unopened retail box. $29
Champions of Krynn Cluebook (SSI) $19
Repackaged versions of Pool of Radiance and Champions of Krynn are also listed.
4Jays.net / 4jays.com lists several Commodore 64 SSI games on their website. I can't tell if these are new or used.
B&C Computer Visions lists several new Atari 8-bit and Atari ST SSI games on their website.
I have had good experiences with eBay for buying SSI software including some that is still shrinkwrapped. The oldest titles tend to get exorbitantly priced (Computer Bismarck, Imperium Galactum, and Geopolitique 1990, for example, are all titles I'd like, but that regularly go for well over $100.) However, titles from the late 1980s are often readily available.