As far as BofA's 99/500 CC, once the CC graduates, you should receive an unsecured CC with a higher CL than the one you have now (as long as you have maintained the CC responsibly). Your deposit will be returned to you.
WaMu does not give customer initiated CLIs. You simply have to wait for them to auto CLI your CC.
Never had Chase Freedom or Pen Fed. Pen Fed, from what I hear, is pretty good to work with. Call the back-door number and speak to a credit analyst. They'll inform you if there will be a hard pull or not for the CLI.
Amex -- HA! Don't even waste the time. You may end up getting your CC closed for some unknown reason. Request at your own risk!
Depending on the type of CC you have with CapOne, you may or may not be eligible for a CLI. If you have one of those "never gonna get it" CCs, don't hold your breath. However, you won't know what type you have until you actually call to request one. This may or may not result in a hard pull.
Citi - I'll wait for others to chime in on this one. Chase as well.
All the best!