I would stick to using all of the same wiring stndard just to make things easier. However the only ill effect of mixing would be that if you are using CAT 5 and CAT 5e/6 you won't be able to get gigabit speeds. I don't know how much of an issue that is to you. If you are only using the CAT 5 as patches it would be easy enough to replace them at a later date if you want to upgrade.
Phones can be wired using CAT 5 no problem. They only use one pair of wires per line so if you are doing a simple single line phone you will have some extra wires there. I forget off hand which pair to use for wiring a phone, but you would need to look that up to make sure it works.