This is a fairly old question, but it popped up on my google search, so here's a partial answer.
To stash select files:
- Stage the files you want to stash.
- Then stash all files, but making sure that 'Keep staged changes' is checked.
- Now you only have the files you want to stash in your current working copy.
- Stash all files, with 'Keep staged changes' unchecked.
- You can then re-apply the first stash, and discard the files that you wanted to stash.
From here. Kind of awkward, but it is what it is.
I suppose what I would do is apply the whole stash without deleting it, use the above procedure to stash only the files you want to apply, discard everything, then apply the partial stash you built.
On the command line, you could probably short-cut a few steps, I suppose...