I have a question on MTU and Mikrotik. On the Wiki there is an article that explains the L2MTU on all versions of routerboard and also shows examples of what the MTU would be with VLANs, MPLS, and VPLS.
Here is where my confusion is… If I create a VPLS tunnel, do I need to adjust the MTU on the VLAN and Physical Interface the traffic is going over to account for the layers, or does the Mikrotik automatically do this for me based on the MTU set on the VPLS interface?
don’t trust auto MTU 
My setup:
l2mtu (of interface) Minimum 1600
MPLS mtu: 1560
VPLS l2mtu : 1525
VPLS IP mtu: 1510
(yes, I know. its just to simplify, easy to remember and don’t make any sense, but, it will work)
L3 MTU (just MTU on Mikrotik) should not be touched on any interfaces, ideally you want to keep an uniform L3 MTU of 1500 through your whole network.
Adjust your MPLS MTU and L2 MTU to account for what size frames you need.
Watch this presentation, there is a segment dedicated to MTU:
http://tiktube.com/video/KHhE3aEKdDoDEJmpIHJwFzJsDlIoFqoq=
Example: full size frame (1500) inside a PPPoE session carried by a VPLS tunnel inside of a vlan; the MTUs are covered on the page 19.
In that case:
ethernet MTU 1500, L2 MTU 1534
vlan interface MTU 1500, L2 MTU 1530
MPLS MTU 1530
VPLS interface MTU 1500, L2MTU 1508