I am still working through a full electronics fit out on a new boat where I've gone through a number of the questions you are posing. It's covered in a number of blog entries starting here
Adventures of Tanglewood: December 2012. You may arrive at different decisions, but I always find it useful to see what other people decided and why.
I'll put in another plug for Rose Point's Coastal Explorer. It's really first rate - I think much better than MaxSea, as well as Nobletec which is now part of MaxSea and slowly turning into MaxSea along with all it's bugs. I run mine on a Mac Mini using VMWare Fusion to run WIndows 7 and Coastal Explorer, and MacOS to run everything else It's flawlessly reliable so far. I also hacked the Mini to run straight off 12V DC (not for the faint of heart, but it works great and draws miniscule amounts of power). That plus a 24" widescreen daylight brightness monitor and it's the best nav system I've ever had. The 24" daylight monitor (DC powered too), Mac Mini, and Coastal Explorer cost about the same as a single Furuno MFD12. Plus you can run CE on up to three computers so you can load it on your laptop for home and planning use, or just as a backup.
Regarding laptops, they have a lot of pluses, but I have found it awkward to find a good location for one, the screen is never bright enough, and I don't like all the power and data cords draped all over the place. I think some form of built-in solution with a daylight monitor is much better.
Back on the Chartplotter vs PC software question, the one big material difference I have found is Radar. All the big vendor's radar data format is proprietary and can only be displayed on their chart plotters. I don't know of any PC nav program that, on it's own, can overlay or display the radar from Furuno, Simrad, Garmin, Raymarine, etc. Coastal Explorer has support for an odd-ball vendor's radar, but not any of the big guys. MaxSea can overlay Furuno radar, but only if you also have a Furuno MFD.