I'm currently fitting our kitchen base units to the existing timber floor, the floor finish is going to be tiled, I believe in only tiling up to the unit legs (then fitting the plinths)  rather than all the way through, would I be better fitting the base end panels after the tiles are down so they are fitted neatly to the floor?

Yes, floor first but I also like to tile the whole floor before fitting the units so that appliances can be moved out and if there is a leak it will be visible sooner.  Also if you rearrange the kitchen the floor will be complete.

Yes, depending on the end panel type you would have a very awkward junction between the plinth and end panel and floor tile otherwise

1 minute ago, Mr Punter said:

Yes, floor first but I also like to tile the whole floor before fitting the units so that appliances can be moved out and if there is a leak it will be visible sooner.  Also if you rearrange the kitchen the floor will be complete.

Yep agree, tile the lot and don’t worry about missing tiles etc

 

however .... I’ve seen a couple recently where they fitted the end panels and on a tiled floor they used 2mm silicone bumper “dots” on the bottom edge of the end panel to lift it slightly. 
 

Then all you do is a bead of clear CT1 under the edge and it is both sealed to the floor but also slight off the floor so should be protected from water. 

I have always done as PeterW above. 300+kitchens and never a complaint. (I make sure i move ever 3 months, and never leave a trail) ?

As well as tiling the lot before fitting the units, I also stuck 50mm x 50mm white PVC angle in place of skirting behind all the units.  This angle is bonded to the floor and wall with sealant, so if there should be a leak anywhere then it shouldn't be able to get to the bottom of the plasterboard.  This also made things easier to clean up when I was fitting things, as it sealed up the small gap between the floor tiles and the wall.

19 minutes ago, Jeremy Harris said:

As well as tiling the lot before fitting the units, I also stuck 50mm x 50mm white PVC angle in place of skirting behind all the units.  This angle is bonded to the floor and wall with sealant, so if there should be a leak anywhere then it shouldn't be able to get to the bottom of the plasterboard.  This also made things easier to clean up when I was fitting things, as it sealed up the small gap between the floor tiles and the wall.

Sealing up like above is good, as it stops the ants finding a route into your kitchen. Once the buggers get in, it is a right pain to try and seal up afterwards. My daughter has a huge fear of ants, so as i was doing her property, every single little gap that i found, was filled with silicon

1 hour ago, Jeremy Harris said:

As well as tiling the lot before fitting the units, I also stuck 50mm x 50mm white PVC angle in place of skirting behind all the units.  This angle is bonded to the floor and wall with sealant, so if there should be a leak anywhere then it shouldn't be able to get to the bottom of the plasterboard.  This also made things easier to clean up when I was fitting things, as it sealed up the small gap between the floor tiles and the wall.

I have done the same in my utility room as well, I don't want a washing machine leak letting water under the sub floor.

 

Agree with others, tile the whole lot.  If you are running short on tiles you can even tile under the units with leftovers or not worry about matching a pattern. Anything is better than nothing.