These are just a few things that would be nice, maybe for a version 2.0. I haven't looked into the internals too much to see how viable it would be to add these features on.
More wire colors - 3 colors are ok, but I could see wanting 4 or 8, which would allow for a 4-bit bus. 8 would permit 8-bit buses. I assume colors are meant to mimic multi-layer PCBs?
Bus lines/Bundles - carry multiple signals along a single trace, like bundled cables. Could also come in colors like wires to control connections. The "cost" to build would be the same as as many individual traces, but would be a lot cleaner when you need to move groups of signals around.
Named Nodes/Tunnels - Each given a name/number all instances are treated as linked. Again, makes moving signals across a board easier. See Tunnels
More advanced Logic Units - These get a bit tricky as some will have more than 4 I/O pins, so the might need to take multiple "nodes" on the board (I would suggest 2x2 which would accommodate two possible connections per-side).
Full Adder w/ carry in - A, B, carry in, carry out and output.
Demuxer - Could even be a 1-bit: A, B, Control, Out
Bus-based gates - Same set of logic gates (and adder/demuxer), but support multiple channels in one component.
Decoders, Negators, Subtractor, Bit shifters (Buses only), etc. would be nice, but are a lower priority.
Plexers
Arithmetic
Flip-flops
Shift Register