The Fluxx Wiki has lists of the composition of the various decks linked off this page.
Here's my attempts at answering your specific questions:
Cards in v2 not in v3:
Doughnuts
The Eye
The Pyramid
Taxes
Coffee & Doughnuts
Death & Taxes
The Great Seal
The Mind's Eye
Money (No Taxes)
Pilfer the Trash
Trash Hand Limit
Trash Keeper Limit
Brain Bonus
Final Card Random
Government Cover Up
Hand Limit 3
Money Bonus
Secret Data
Tax Bonus
Time Bonus
New cards in v3:
Sleep
Baked Goods
Bed Time
Dreamland
Hearts & Minds
Rocket Science
Squishy Chocolate
Winning the Lottery
Empty the Trash
Go Fish
I Need a Goal
Jackpot
Let's Do That Again!
Let's Simplify
No Limits
Rotate Hands
Double Agenda
Reverse Order
First Play Random
No-Hand Bonus
Poor Bonus
Rich Bonus
Inflation/X = X + 1
The Looney Labs newsletter from Nov 14, 2002 explains the changes in v3.0 this way:
1.) What will be different? Roughly half of the cards in the deck have changed in some way, but in many cases the revisions are so minor that only a few people will notice them. Over 25% of the cards have been radically changed or are completely different.
2.) Can you be more specific about what's changing? The 4 "Bonus" rules have been replaced with a trio of stronger ones, called the Rich bonus, the Poor Bonus, and the No-Hand Bonus. The 3 new rules which we made into promos for Origins 2002 (X=X+1, Double Agenda, and Reverse Order) have all been added. Those annoying "hide a Keeper" rules are all going away, and we're getting rid of 4 rather wimpy Actions and putting in 7 better ones. We thinned the Keepers down a bit, increased the number of Goals, and made sure no Keeper was useful for only 1 thing. The 5 Keepers being dropped are the Eye, the Pyramid, Coffee, Donuts, and Taxes, but in their place we're adding 2 totally new ones: Sleep and Dreams. Changing the Keeper mix required us to drop a number of Goals that no longer made sense, but of course others were needed for the new Keepers. A couple of Goals also got renamed. Other minor changes included replacing the artwork for War (as I described a few weeks ago) and for Chocolate (since we've learned that a certain powerful Chocolate Corporation has strong attitudes about their trademark on a little slip of paper sticking out of a piece of candy). Final Card Random has been changed to First Play Random (it works better), the blank card has been eliminated (it's obsolete), and the rules insert will be larger (featuring the cartoon shown here). The tuckbox will be the same size, but it will look a bit different; the 6-pack display carton will change only slightly. To sum up: it's way better than before.
Looking further at the v3.x page, I think these are the minor changes:
- The chocolate keeper has a kiss in 3.0 and a bar in 3.1
- The 3.0 "The Sun & the Moon" goal is called "Night & Day" in 3.1
- The "Go Fish" and "I Need a Goal" actions are only in 3.0
- The "Jackpot" action is only in 3.1
- The 3.0 "X = X + 1" rule is called "Inflation" in 3.1
- The 3.1 Fluxx packaging included another card to "Join the Fluxx Fan Club"