Hi
I really need some help here getting my MTU settings right.
In my network I use VLANs, QinQ, EoIP tunnels, and planning to use MPLS VPLS.
I see now, using for example EoIP, packets are fragmented, and 2000PPS in becomes 4000PPS.
What MTU settings should I use in the network to carry these services?
1st off – for the most part if you’re using Routerboards the L2MTU is the important aspect. For non-mikrotik units however some trial and error may be required.
Rule of thumb 1 - When using MPLS … configure the biggest bloody MTU your gear can handle 
Rule of thumb 2 - Each MPLS label/VLAN will add 4 bytes
The MPLS aspect adds complexity as each tag you add should add 4 bytes - so if you have an environment with tons of tags your MTU would have to grow to accommodate it.
If you’re carrying QinQ VLANs inside your VPLS then lets take baseline example:
If you have a funky network card you may have to account for the ethernet frame overhead itself (14 bytes)
Ethernet MTU 1500 + 4 bytes for VLAN + 4 bytes for QinQ VLAN + 4 for VPLS + 4 MPLS + 4 MPLS (2nd tag) = 1530
If we now add EoIP to the mix — 8bytes GRE, 14Byte ethernet, 20byte IP = 42 bytes overhead
If we combine/mix that all together your L2MTU support could require 1572 bytes…
EDIT: Found this after writeup - http://wiki.mikrotik.com/wiki/Maximum_Transmission_Unit_on_RouterBoards (might help you a bit )
So, in summary - as per Rule of Thumb1 — go BIG Also remember to try set same MTU everywhere you are going to run MPLS