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I have a suggestion, one that I hope is easy to implement.

In info page for each genre, instead of having the "puzzles in this genre" link you would have the "puzzle navigation bar" just like in individual puzzle pages.

This is helpful because:

1. This page is viewed by those who are new to the genre, and are learning about it for the first time. Many of them would like to start out with one of the easiest puzzles, just to get the hang of it.

2. This page is also be useful to bookmark by someone who is currently into the specific genre, solving all the puzzles. This way one could easily pick off with the next unsolved puzzle, or chose an unsolved puzzle of a level of one's choosing.

Ok, then, Thank you Maarten.

Dragging a number is the easiest way to fill a cell.
If a user changed the color he is solving the puzzle and then uses dragging, I don't think that he usually wants to change the color of the original cell; he just wants to save time and effort.

Dragging black cells would be really helpful, especially when large numbers are placed there. This way one wouldn't normally need the keyboard shortcut, and can only use the mouse.
The color of the target cell should, of course, be determined by the current user color.

In my opinion, separators are much more helpful to the solution process than connector, therefore the left click should be for separation, not connection.

The use of borders as connectors is beautiful. Also, it can really help new Fillomino solvers to get the idea.
There are almost no cases where manually adding the connector is helpful for the solving the puzzle; after all if, you placed a connector next to a solved cell, it means you can immediately solve the cell it connects to. There are relatively few cases where you would want to indicate that adjacent empty cells must have the same value.
For these reasons I think these connectors should be automatic.
If the choosing the color of the connector automatically is an issue you can peak a neutral one, or average the RGB values of the two cells.

Thank you Johan for the crafting the Fillomino applet. It is really beautiful.

I have a few usability suggestions; I'll post each one as a separate post so it will be easier to keep track of them.
Please don't think this means I don't like your work; I like it, and I really appreciate it.

It's interesting that mathgrant write to check only for the boundries for correctness, I though to check only the numbers; however I often solve fillominos on paper and forget to fill some numbers. I guess boundries are better, but only if they would also be automatically deduced from neigbours with different numbers; they don't have to be filled in visually, they may only be inferred for the checking procedure.
Another suggestion for the applet would be that you can drug a number into other cells continously to fill other cells just like you would color cells in the LITS applet.

I would love to see Fillomino, especially since I'm trying to author some of those.
writing an interactive form of the puzzle may be a bit difficult since borders, as well as grid cells need to be edited to solve this puzzle type.