I have an x86 Mikrotik router with three WAN connections, each WAN IP is on different subnets with different gateways.

Only one of them will respond to remote pings, there is nothing in the firewall that would prevent the pings.

How can I make the Mikrotik respond to pings for all 3 ip's

it's responding, but it's using the default gateway to send the replies... so if it comes in WAN2 or WAN3 its replies are going out WAN1 I am guessing. With tcp and udp you can mangle and packet mark, however with ICMP i have never reliably gotten that to work right.

you have to mark connections (where they come in and then using connection-mark mark those connections back to interfaces they originated and set up default routes accordingly

Just enable those 3 gateway as your default gateway.

Hope it will work .

Rafiq...