Line an 8x8 or 9x9-inch pan with parchment paper; set aside.
In a large bowl, stir together the oats, rice cereal, pretzels, 1/4 cup of the M&Ms, and flax seeds, if using. Set aside.
In a medium-sized saucepan, melt together the butter, honey, peanut butter, and brown sugar. Bring mixture to a boil, then simmer on medium-high heat for 2-3 minutes, stirring frequenty. Remove from heat and stir in vanilla.
Pour mixture over dry ingredients and stir with a wooden spoon. Everything should be evenly coated and well-combined.
Scrape mixture into the prepared pan, and press firmly to pack it evenly across the bottom. When the bars still have a little give to them, sprinkle the remaining M&Ms on top, then press again lightly to help the M&Ms adhere and pack everything else in very tight.
For the best consistency, refrigerate the pan for 30 minutes before lifting out the parchment, cutting, and serving. Bars keep best stored in an airtight container in the fridge.