In a nutshell....
A4000 gives you AGA, access to cheaper IDE drives, and room inside for two hard drives, two floppies, and a 5.25" drive (optical drive though this would remove one hard drive since IDE can only handle two drives) and for RAM uses easier to get SIMMs instead of ZIPs to expand its Motherboard to its max. 3000 only has room for two hard drives and two floppies no 5.25" internal. Oh, and that SCSI cable is honking huge!
Now, AGA isn't as big a deal if you intend to get an RTG graphics card but then nor is the scandoubler of the 3000 since your VGA monitor would be plugged into the graphics card at that point and the better, later, Zorro III RTG cards have scandoublers assuming you can get them.
SCSI in the 3000 gives you access to old Scanners, tape drives assuming you intend to use these. If not really it gives you nothing and SCSI can be added to the 4000 at the expense of a slot and the only floppy drives you can really use internal have to be designed for the 3k due to having to conform to the faceplate of the machine. 4k has an open rectangle for internal drives so your available drive pool increases to just about any Amiga drive that fits a standard drive space.
3000 is better looking and with RTG can run almost everything the 4k can. a 3k will never run any AGA only software (stuff that bangs hardware) and never use a Video toaster 4000 the same way a 4000 can (not that you are probably considering that).
RTG with builtin scandoublers are the Picasso IV and Cybervision 64 cards (of course, since these are separatable parts to allow the card to be used in the 2k which does not have its video slot in line with Zorro, make sure if you get one that it includes the scandoubler card if broken off to install in a 2k. I have heard of people buying them assuming the scandoubler comes with it and finding out later it doesn't). Ones that done have it are Retina ZIII
3000 pros probably cheaper, better looking, scandoubler, SCSI for non hard drive applications, same zorro III for better RTG cards that 4k has, built like a tank.
3000 cons 030, harder to get ZIP ram on mobo, custom floppy drive slots, scandoubler made redundant by RTG cards that include one, built like a tank (hard to work inside)
4000 pros AGA for games that need it, 040 standard on many models, IDE for cheaper drives, more drive bays, standard Floppy bays, SIMM RAM on mobo, more open inside for access (RAM on ZORRO side instead of under drives) Zorro III, no scandoubler to be made redundant by RTG card (depending on wether what you get has built in or not).
4000 cons tend to be more expensive, watch out for the buggy 3.0 '040 card and rev 9 Buster that has issues with Zorro III cards and '040 hitting the RAM at the same time causing lockups make sure you get a 3.1 card and rev 11 Buster - 030s never have this issue nor do third party CPU cards (at least I don't think they do), RTG better than AGA as long as software supports it, less of a tank (not as well built and some parts more flimsy) no scandoubler.
Great site for 4000 info:
http://www.wonkity.com/~wblock/a4000hard/main.html
