The regular Matlab function call stack is itself a stack of workspaces. Just using functions is the easiest way to use one, and Matlab's copy-on-write makes this reasonably efficient. But that's probably not what you're asking.
There's a natural correspondence between workspaces and structs, since the same identifiers are valid for variable names and struct fields. They're both essentially identifier => Mxarray mappings.
You can use whos and evalin to capture workspace state to a struct. Use a cell vector to implement a stack of them. (A struct array won't work because it requires homogeneous field names.) The stack could be stored in appdata to prevent it from appearing in a workspace itself.
Here are push and pop functions for this technique.
function push_workspace()
c = getappdata(0, 'WORKSPACE_STACK');
if isempty(c)
c = {};
end
% Grab workspace
w = evalin('caller', 'whos');
names = {w.name};
s = struct;
for i = 1:numel(w)
s.(names{i}) = evalin('caller', names{i});
end
% Push it on the stack
c{end+1} = s;
setappdata(0, 'WORKSPACE_STACK', c);
function pop_workspace()
% Pop last workspace off stack
c = getappdata(0, 'WORKSPACE_STACK');
if isempty(c)
warning('Nothing on workspace stack');
return;
end
s = c{end};
c(end) = [];
setappdata(0, 'WORKSPACE_STACK', c);
% Do this if you want a blank slate for your workspace
evalin('caller', 'clear');
% Stick vars back in caller's workspace
names = fieldnames(s);
for i = 1:numel(names)
assignin('caller', names{i}, s.(names{i}));
end