How Has The Fluxx Core Game Changed Over The Years?
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 &amp; Doughnuts

Death &amp; 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 &amp; 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 &quot;Bonus&quot; 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 &quot;hide a Keeper&quot; 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 &quot;The Sun &amp; the Moon&quot; goal is called &quot;Night &amp; Day&quot; in 3.1
The &quot;Go Fish&quot; and &quot;I Need a Goal&quot; actions are only in 3.0
The &quot;Jackpot&quot; action is only in 3.1
The 3.0 &quot;X = X + 1&quot; rule is called &quot;Inflation&quot; in 3.1
The 3.1 Fluxx packaging included another card to &quot;Join the Fluxx Fan Club&quot;