Again, the official "limit" per list  is 2,000 items. BUT, Microsoft
has ended up saying that as long as you don't display more than 2,000
items in one VIEW, then you'll be okay. The real limit is somewhere
around a couple of million. So, FILTER THE VIEWS. (especially the
default ones)

Here's a really good whitepaper that goes into (very technical) detail
about large lists:
go.microsoft.com/fwlink/?LinkId=95450&clcid=0x409

You also have a question about folders...
Folders aren't really the way to go. I believe the best practices is
to use metadata (list columns) to organize  the data instead.

Oh, and if you want to customize the solution  before deploying it,
you can first do your customizations, and then save the site as a
template, and then deploy THAT one to your environment.

More specifically, it's a guideline for best performance - 2000 items is
where performance starts to degrade, and it does so at a non-linear
rate. On folders - a folder is really just a view at it's core, so
there isn't really a significant performance difference between
organizing via indexed metadata columns and using folders.

According to

technet.microsoft.com/en-us/library/cc262787.aspx

performance is significantly better (comparing transactions per
second) using folders compared to indexed metadata (unfortunately).

Interesting - I hadn't seen that comparison obviously. J It's counter
to the information I was given a while back by my Microsoft contacts,
will need to do a little follow-up I think...