For one thing, we do have a way to cross-promote products based on the item(s) being purchased, although this only happens on the thank-you page after the initial checkout is completed:
http://www.e-junkie.com/ej/help.cross-promo.htm
You can also add custom HTML -- such as a link to another product page or even an Add to Cart button for a specific product -- inside the overlay-style cart itself, and this can even differ when the cart is displayed in one page vs. another. Just add these lines to your View Cart code on each page, just before the "// -->" line in the standard code you obtained from Seller Admin:
function EJEJC_config() {
EJEJC_POSTCALL=true;
}
function EJEJC_shown() {
jQuery("#tdPmnt").attr("innerHTML",
"Any <b>HTML</b> you want to add in the cart goes here on one long line");
}
Note that any custom HTML you add must be strung into one long line, any "double quotes" should be either changed into 'single quotes' or preceded with a \"backslash\", and any ampersands (&) should also be preceded with a backslash (\&).
If you are already using the functions EJEJC_config(){} or EJEJC_shown(){} for other cart customizations, just add in the proper places any lines above which are missing from your current customization code.
For a more sophisticated solution, you might investigate what MUVenum has done:
http://muvenum.com/buy-now/
There you will see they have devised a way that, when a download item is added to the cart, a "Backup CD" upgrade link is shown in the cart, and if that item is added to cart and then the original download item is removed, that also removes the CD upgrade. You would need to examine their page source or contact them for advice to find out how they accomplished that trick.