Is their anyway for you to make a portal that only allows a one WSC, nothing else? No cameras, turrets, Chell, etc. I know for no Chell you would make a playerclip, but I don't have any idea how to make anything else.

maybe with a filter entity?

You will need several things, just in front of the portal.

1. A brush textured with playerclip to stop Chell from getting through.

2. A brush textured with the invisible texture, tied to func_clip_vphysics. This will stop everything from getting through, until you do step 3.

3. Create a filter_activator_name, give it the name filter_box, then in the filtername value, type in the name that you have given the storage cube. Go back into your func_clip_vphysics, and in the filtername value, type in filter_box. Either in the func_clip_vphysics or the filter_activator_name, there will be something that allows you to select the option of Allow or Disallow. Select the Disallow option.

What you should have now, is a a serious of brushes that you can't see, but will stop anything from passing through into the portal, except for the cubes.

Is their any way to allow only one cube?

you can name your cubes "cube1" "box1" etc etc. and in the filter use that name to either "allow"/"deny" whatever you do/don't want to go through

place a trigger on the other end of the portal, with the filter of the cube.
When it is triggered, it should close the portals.
That way nothing can go trough again untill the portals are reactivated.

Or when it is triggered, it enables a brush which indeed does block cubes.
No way to get the cube back that way but I don't know what u want...