Best endurance exercises for legs

I've heard skipping could be good for the calves.

Or uphill.

Yes.  "Uphill" provides the resistance instead of speed/wind.

I'm hesitant to recommend cycling for purposes of improving table tennis, even though I very much enjoy cycling anyway.  I have a couple of friends that are former professional racing cyclists and they both still have exceptionally strong legs.  That is, I find that their motion for small footwork to be inefficient.  That is, if you need someone to run down a ball 12 feet away, they'll both do great, but if you move the ball over 2 inches, they tend to lean rather than do the micro-footwork needed.

That said, I would recommend a mix of methods:

1) Cycling that includes hills and/or interval training (this is where you change your cadence).

2) Stair climbing, or jumping rope, or even elliptical machine (assuming you have an elliptical that requires a high leg lift or uses an inclined plane such as Percor).

3) Squats with weights.

I agree.  You don't want to do only cycling.  After cycling I do a driving pitter-patter routine on my toes where you alternatively drive your right and then left foot as quickly as possible while in a semi-squat position.  Coach Li calls it "tippie-tap" (as near as I can understand what he's saying.)  The idea is to do this at a very high speed.   I think this helps with the small steps you are talking about.

That's not surprising - so long as good form is used and you don't train for maximum lift.  

One of the reasons I started doing hill climbs on the bike is for the out-of-the-seat climbing.  That workload,  is similar to doing heavy leg work such as squats.  I find the hill climbs are therapeutic for my knees. 

Ichiro Ogimura was fond of leg work as well.