Many of them allow it, so just use a vendor that does. I know iTeadStudio explicitly allows it and does free v-scoring (they have instructions on how to order it properly), and DirtyPCBs allows it on 2-layer boards. But only panelizing the same design.
They only do free v-scoring for 50+ boards, as do others. But for their 10 PCB prototype service their charges are even more ridiculous than most. Their panelization/sub-PCB rules are clearly described here:
http://support.iteadstudio.com/support/solutions/articles/1000160585-pcb-panelization-rulesLike the other suppliers they also allow multiple designs on one board, but you can't use slots or holes as separaters and you can't have a slot longer than 2/3 of the panel length/width. Fair enough. But make that slot slightly more than 2/3 or you want one v-groove your 10 5x5cm boards at $9.9 will cost an additional $20!! (Actually for panelized boards they require them to be > 8x8cm so you'd have to buy >= 10x10cm boards at $19.9+)
Now look at 2 (a) & (b) in that link. If you have 5 panels of 4 or 5 different sub-PCBs you incur an extra charge of $80 for the 3 v-grooves in that example!!! So $19.9 for 10 10x10cm boards + $80 = $99.9. But if each of your sub-PCBS were less than 5x5cm, you could get them as separate PCBs for half the price at 5 x $9.9 = $49.5!
As I understand it, they don't differentiate between panels or sub-PCBs so if you wanted them panelized into 5 identical panels they would still cost $99.9. But since you are now ordering 50 panels in total, the alternative would be to buy 50 5x5cm boards at less than a third of the cost for $30.65! Of course you'd lose the advantages of panelization with this option.
As the number of panels/sub-PCBs increase the disparity gets even more extreme; a surcharge of $140 for 8 panels?!!!
Many seem to have similar pricing/policies so I must be missing something significant, but this pricing seems bizarre.
I'm not sure if any will allow multiple designs within your $area purchase. They're selling flat rate within a specific area, not flat rate for a certain area. This seems fair to me, since it generally costs more to order from places that bill by area, though I'm not quite sure of the economics behind that. I assume it's just averaging, and their choice of whether to allow multiple designs / panels or not will affect the average price.
They do allow multiple designs for free so its nothing to do with averaging - its just that you get hit with excessive charges for v-grooves or slots > 2/3 width or length.
I see that dirtypcbs allow 2-layer panelized boards but don't do v-grooving - so not even an extra cost option.