Someone needs to get the ball rolling in these forums, so I thought I would start.
I will write and add / edit this over the next few weeks...
The PC-88 series was a fairly powerful Z80 based machine but NEC wanted to push into the 16bit business PC market and made the PC-9801 series in 1982. These machines ran a NEC made 8086 and had a 640x400 mode in 8 colouirs with later machines using a V30 and offering 16 colours from a palette of 4096 colours and then the 286, 386 and 486 series chips up until the eraly 90s. These machines were more speced then the original IBM PC but were not PC compatable, although they were MS-DOS compatable so well behaved programs that used MS-DOS calls rather then hitting the hardware directly would run. The early PC-9801 machines
The NEC-9821 was NEC attempt at a machine that was PC-9801 compatable, still not PC compatable but had more Windows compatabilty and more PC features, for example IDE drives were supported rather then the clunkcy SCSI drives of the 9801 series. You can run most PC-9801 software quite happily and you could run a special version of Windows 98 and Windows NT on it, there are versions of Direct X (up to 5) that will work on it so you could play early Windows 98 games on it qutie happily.
Generally if you are going to buy a PC-98 series machine there is no reason to get anything other then a PC-9821 series PC. You also have a choice of two flavours desktop and notebook PCs (which are called Lavie, although later machines also carried this name and are standard Windows PCs....)
Easier to expand, so if you feel the need to plug in the NEC PC-FX card then you can.
Can use any of the sound cards.
Easier to upgrade as it uses fairly standard parts
Some have the monitor built into the system
Fitting 5.25 drives is quite easy and you will find machines with dual 5.25 and 3.5 inch drives
Most way a ton, so they will cost a lot to ship from Japan.
More likely to be damaged on way from Japan.
Only the later cards / machines had VGA ports so you may need an adapter or import a monitor to use the machine.
You will need to make sure you have a Keyboard and a mouse as they do not use standard ports.
Machines are lighter so are cheaper to post
They have 16bit PCMCIA card slots so you can transfer software easier using CF card readers.
This also means you can get Network, USB (requires Windows 98SE and you can only use mice and keyboards once the machine has booted up) and even WiFi (only b though), these generally on Windows and require PC-98 drivers.
They used standard IDE 2.5" drives so it is easier to swap them around so you can multiboot OSes without having to reconfigure or try to partition the drive.
Has nice TTF displays
Later machines have dual voltage PSUs
Early machines do not standard VGA ports so you need an adapter or just the internal montor
Machines had a 640x480 or 800x600 display, so DOS based games will have black borders on 800x600 dispaly and Windows looks like arse on 640x480 based machines
Most machines have one slot for a CD-ROM or Floppy Disc module, but expanders existed so you could use both.
Later machines only had Windows Sound System so DOS based PC-98 games would be silent.
You do need the Hard Drive caddy to swap hard drives.
Attaching 5.25 drives is more difficult (although not impossible)
Not all machines have TTF displays so you could get a DSTN display which looks washed out.
Earlier machines have 100V only PSUs...
The PC-98 does run a version of MS-DOS, so you do need to write basic CONFIG.SYS and AUTOEXEC.BAT files for the CD-ROM to work and for the machine to load drivers for hardware you have. Running Windows means you can not run a lot of MS-DOS based software easily.
The PC-98 series does have a lot more adult software then the FM Towns and X68000 series machines and it does have less arcade based software then it's rivals but there are games out there, however there are good games out there.
Transfering software from emulator sites to the PC-98 is quite easy depending on your set up. I have for example ran Windows 98 on a 32mb PC-9821 Lavie NR-266 machine and connected to the internet using a ethernet network card, downloaded the floppy image files, used a program to convert them to floppy files and wrote them directly to disc.
However a USB floppy drive on a Windows PC is enough for you, and the FORMAT command in a command prompt (even on Windows 7) and two programs is enough for you to write floppy images, you can even back up your discs this way too. I did this.
Once I get my machines out, I will write some more on this...