Correct Episode Order
Here's the order of Dinosaurs episodes based on production #s, followed by the order they were originally aired. On one hand, the production # order gives you an idea of what they might have originally intended. On the other, you are stuck with more back-to-back character-centric episodes. For example, the two Robbie episodes at 343/344. Even so, the original airdates had tons of Baby-centric episodes in the mix--especially within season 3 and 4--so it goes both ways.
Finally, it's worth noting that "Employee of the Month" was made for season 1. Also worth noting: season 4 was mostly scrapped. Even if the "lost episodes" weren't cut, it still would have been a short season--14 episodes--compared to 2 and 3.
Season 1 (1991)
Season 2 (1991-1992)
Season 3 (1992-1993)
Season 4 (1994)
Unaired Episodes
301--1.1 The Mighty Megalosaurus
302--1.2 The Mating Dance
303--1.3 Hurling Day
304--2.6 Employee of the Month
305--1.4 High Noon
306--1.5 The Howling
307--2.4 Charlene's Tale
308--2.5 Endangered Species
309--2.3 I Never Ate for My Father
310--2.1 The Golden Child
311--2.2 Family Challenge
312--2.7 When Food Goes Bad
313--2.16 The Clip Show
314--2.8 Career Opportunities
315--2.9 Unmarried...With Children
316--2.10 How to Pick Up Girls
317--2.11 Switched at Birth
318--2.12 Refrigerator Day
319--2.13 What 'Sexual Harris' Meant
320--2.17 A New Leaf
321--2.14 Fran Live
322--2.15 Power Erupts
323--2.18 The Last Temptation of Ethyl
324--2.19 Nuts to War: Part 1
325--2.20 Nuts to War: Part 2
326--2.22 Slave to Fashion
327--2.23 Leader of the Pack
328--2.21 And the Winner Is...
329--2.24 WESAYSO Knows Best
330--3.3 Network Genius
331--3.1 Nature Calls
332--3.2 Baby Talk
333--3.4 The Discovery
334--3.18 Dirty Dancin'
335--3.6 Germ Warfare
336--3.12 Getting to Know You
337--3.7 Hungry for Love
338--3.8 License to Parent
339--3.5 Little Boy Boo
340--3.9 Charlene's Flat World
341--3.10 Wilderness Weekend
342--3.14 Out of the Frying Pan
343--3.11 The Son Also Rises
344--3.15 Steroids to Heaven
345--3.13 Green Card
346--3.16 Honey, I Miss the Kids
347--3.19 If I Were a Tree
348--3.20 We Are Not Alone
349--3.22 The Clip Show II
350--3.17 Swamp Music
351--3.21 Charlene and Her Amazing Humans
352--x.xx Into the Woods
353--x.xx Scent of a Reptile
354--4.1 Monster Under the Bed
355--x.xx Working Girl
356--4.2 Earl, Don't Be a Hero
357--4.6 The Terrible Twos
358--4.3 The Greatest Story Ever Sold
359--x.xx Variations on a Theme Park
360--x.xx Life in the Faust Lane
361--4.5 Earl's Big Jackpot
362--x.xx Earl & Pearl
363--x.xx Georgie Must Die
364--4.4 Driving Miss Ethyl
365--4.7 Changing Nature