Is 2mb of L2 cache better than 3 mb of L3 cache ?

Although I have not run any benchmarks, I would say this:

For games pick L2 cache (faster)
For spreadsheets/databases pick L3 cache (size)

More lower level (lower number) cache yields faster performance.

If I had to make a choice, I'd always choose the option with more L2.

I'm going to say doesn't make a difference/not enough info. There were some L3 cache P4 EE chips that are still junk compared to chips of today. Having L3 cache doesn't make it good/bad.

it really depends on what CPU's your comparing. sounds like you want to compare 2 completely different cpus, such as this http://www.anandtech.com/bench/Product/59?vs=97

This looks like an apples and oranges comparison. For example, Core2 CPU's do not have an L3 cache.

Which CPU's?

Depends on what cpu it is......

That's like saying what's faster, a V6 or a 4cyclinder. Well that depends on if it's a Honda Civic or a Chevy Suburban.