Ignoring ship specific builds, there are certian upgrades that are considered universally useful. Veterian Instincts on anything PS7 or higher, Push the Limit, Even Squad Leader is starting to get popular as a munitions fix.

What are the most popular cards in the tournament scene, that are used on more than a single ship? (no Falcon titles)

Engine Upgrade. Makes everything better.

Engine Upgrade, Autothrusters, FCS, HLC, Mango Cannon, Adv. Sensors spring to mind

Vi

Predator

Most popular upgrade card is Push the Limit.

The card is found on the following popular lists.

1) Anything running Soontir Fel, Royal Guard Pilot, Carnor Jax

2) Some IG-88 builds

3) Some YT-2400 builds

4) Some Firespray scum builds (Kath + K4 Security Droid + Engine Upgrade + Push the Limit)

These encompass some of the most popular and successful tournament builds.

The upgrade card is also sometimes found on fringe builds.

5) Tycho builds with lots of stress

6) Heavy turtle Howlrunner builds with a Black Squadron TIE Fighter for Wingman.

7) Keyan Farlander B-wing

http://lists.starwarsclubhouse.com/tableau

I think this should answer ALL of your questions.

Just click on upgrades.

VI, Predator, Engine Upgrade are the ones i've seen the most. Lone Wolf has also been used a ton in our local meta.

Soontir and IG-88 are the only places I've seen autothrusters. It's certainly made them both more popular but you don't see this stuff in every list..

Oops Well here are the PIE charts if you like those instead.

Xwing lists juggler charts

Since list juggler tracks only tournament play you can be assured that nearly all the data comes from tournament lists.

So far for most used competitively upgrades the top 5 are:

1. 7.76% Vet Instincts
2. 5.96% Fire Control Systems
3. 5.37% Engine Upgrade
4. 5.35% Push the Limits
5. 4.43% Autothrusters

VI can be used anywhere, FCS you will see that on Brobots (I still call them Buzzdroids) and occasionally on Phantoms. EU is used allot on Decimators and other large base ships. PTL is used on Soontir and other A-wings. Autothrusters is used by Soontir and the Brobots/Buzzdroids.

R2-D2

Yes I know it's rebel specific, but boy is it useful for multiple ships:
Luke, Corran, YT-1300. All rebel Y-wings, X-wings and E-wings can use this little useful bugger.

I've never seen anyone use R2-D2 on a Y-wing.

R3-A2 on the other hand has become pretty popular.