You can purchase non standard size portfolio's for artists that have the protective sleeves in them for larger works. You definitely want to invest in them as getting a piece to look right after its gotten dusty is a nightmare. http://www.jerrysartarama.com/go-see-presentation-books
Alternatively you can wrap them in acid free tissue and paper, just make sure you write the page number and volume on it along with any identifying facts first. You don't want to find that the crappy pen you grabbed has accidentally bleed through onto the work.
For stuff like accrylics that you don't want mushed up with something you can drive thumbnails into the corners that would be covered when framed then place a second one face down on top and tape or rubber band them together before tissue wrapping.
Also, if a work is matted but not framed and you need to move it then definitely create a cover. Just cut piece of acid free paper to the same length as the piece but make it about half again as long width wise so you can tape it to the back, creating a little flip cover for it.
Edit
I forgot, A4 portfolio's are generally available at Asian shops like Daiso Japan for a couple bucks. Cant vouch for them being acid free but I've used them to bail myself out when I had class portfolio presentation due but hadn't budgeted for a better one. Wouldn't hurt to use them to move stuff around but you shouldn't store anything in them long term unless you figure out the acid bit.
I tend to limit my work size in traditional mediums to ones I can easily find a portfolio for. Just makes life easier.