Some people would probably not agree with the disadvantages I listed since I've seen people go crazy with complex build using IC chips and even SMD components on Manhattan style builds.
I try to keep the distance between the middle of the pads to around 8mm-13mm so that the components are tight together, but not too close that is becomes too fiddely to work with. After the pads are made I like to pre-solder all the pads - just fill them up with a decent amount of solder. Now the board is perpared and it's time to start soldering in the components. Cut the legs of the component alittle shorter (check the distance against the board) and bend the legs alittle to make small "feet". Reflow the solder of the pad and put the component in. Hold it and let it cool for a few seconds, then do the other side. As you go along there will often be several components connected to the same pad, and then it helps to apply some new solder to the pad when adding more components. I find that it's best to start in the upper left corner and work your way through the board from left to right.
As you can see in this example, the layout follows the schematic with a few minor changes (just to have the pads lined up nicely). I normally just use pen and paper to make the layouts, but I wanted it clean and easy to read for this presentation.
Parasit Studio originals
I made two original designs specifically for Manhattan style of building. :)
Even through it might seem like a step backward, it's been really fun to make something different for a change. Expanding my bag of tricks, learning and challenging myself to come up with new stuff is what keeps this hobby fun and interesting for me. I haven't seen many pedalbuilder using this technique and I was inspiried to try it from a great HAM radio guy that I follow on youtube.
Check out his channel: https://www.youtube.com/user/w2aew/