I would suggest you to disable some checkboxed from the be selectable with respect of "disabled" attribute. To make full implementation you will need

1. set "disabled" inside of loadComplete event handle
2. additionally prevent selection of disabled rows inside beforeSelectRow event handle
3. to have support of "select all" checkbox in the header of the multiselect column implement onSelectAll event handle which fix selection of disabled rows.

The corresponding demo can you see here. The most important part of the code is here:

var grid = $("#list10"), i;
grid.jqGrid({
    //...
    loadComplete: function() {
        // we make all even rows "protected", so that will be not selectable
        var cbs = $("tr.jqgrow > td > input.cbox:even", grid[0]);
        cbs.attr("disabled", "disabled");
    },
    beforeSelectRow: function(rowid, e) {
        var cbsdis = $("tr#"+rowid+".jqgrow > td > input.cbox:disabled", grid[0]);
        if (cbsdis.length === 0) {
            return true;    // allow select the row
        } else {
            return false;   // not allow select the row
        }
    },
    onSelectAll: function(aRowids,status) {
        if (status) {
            // uncheck "protected" rows
            var cbs = $("tr.jqgrow > td > input.cbox:disabled", grid[0]);
            cbs.removeAttr("checked");

            //modify the selarrrow parameter
            grid[0].p.selarrrow = grid.find("tr.jqgrow:has(td > input.cbox:checked)")
                .map(function() { return this.id; }) // convert to set of ids
                .get(); // convert to instance of Array
        }
    }
);

UPDATED: Free jqGrid supports hasMultiselectCheckBox callback, which can be used to create multiselect checkboxes not for all rows of jqGrid. One can use rowattr to disable some rows additionally. As the result one will get the described above functionality in more simple way. It's recommended to use multiPageSelection: true option additionally for free jqGrid with local data (datatype: "local" or loadonce: true). The option multiPageSelection: true will hold the array selarrrow on paging. It allows "pre-select" some rows by filling the corresponding ids inselarrrow. See UPDATED part of the answer and the answer with the demo for additional information.

Great answer from Oleg, I would also add code to deselect disabled rows, complete onSelectAll function below.

onSelectAll: function(aRowids,status) {
    if (status) {
        // uncheck "protected" rows
        var cbs = $("tr.jqgrow > td > input.cbox:disabled", grid[0]);
        cbs.removeAttr("checked");

        //modify the selarrrow parameter
        grid[0].p.selarrrow = grid.find("tr.jqgrow:has(td > input.cbox:checked)")
            .map(function() { return this.id; }) // convert to set of ids
            .get(); // convert to instance of Array

        //deselect disabled rows
        grid.find("tr.jqgrow:has(td > input.cbox:disabled)")
            .attr('aria-selected', 'false')
            .removeClass('ui-state-highlight');
    }
}

For people (like me) that end up on this answer after searching on Google, there is a very easy solution to this problem since jqGrid 4.0.0.

It's enough to add the css-class 'ui-state-disabled' to the row that you don't want to be selected. See The changelog of jqGrid 4.0.0. And you could still combine that with hiding or disabling the checkbox.

    var $jqgrid = $("#jqgridselector");         
    //loop through all rows
    $(".jqgrow", $jqgrid).each(function (index, row) {
        var $row = $(row);
        if ($row === condition) {
            //Find the checkbox of the row and set it disabled
            $row.find("input:checkbox").attr("disabled", "disabled");
            //add class ui-state-disabled, because thats how jqGrid knows not to take them into account for selection
            $row.addClass("ui-state-disabled");
            //I overwrite the opactity of the ui-state-disabled class to make the row look 'normal'
            $row.css("opacity", 1);
            }
        });