I use Org-mode to organize and track my research. It is an Emacs major
mode that seems to hit most of your requirements. The .org files are
plain text which should guard against bloat and lets you access them anywhere, even when you do not
have Emacs or Org-mode available.
linking to past experiments/pages
Org-mode has linking capability to any type of file, as well as to
specific locations in a document.
Org-mode has support not only for LaTeX equations but for a number of
programming languages via org-babel. You can include the code blocks
inside your .org file.
uploading papers, or other URLs.
Because it is only a text file, this sort of behavior can be
accomplished through the linking mechanism. The links
can be to other documents/papers on your machine or URLs. Visiting a
URL in Org-mode will open your browser to the requested link.
being able to transfer data.
I am unsure what you are looking for here. Org-mode has a nice
built-in table editor with automatic column width adjustment and some
spreadsheet behavior. If you do not want the actual data in the .org
file, you can always link to do the data. If you are looking to import
data into the file directly, Org-mode has a function
will parse TAB or whitespace separated data into an Org table.
dating and version control
I use Org-mode to track my time spent on various research items. You
can set the headings in Org-mode to behave like multi-state TODO lists
and assign time to them. Most headings start as TODO, switch to
STARTED when I clock in on them, and then I can update them to DONE
when I am finished. It can also generate reports based on your tracked time. For example, I use a built-in report for the last week to help generate weekly research updates.
I handle my version control and distribution
through Dropbox, but since the files are plain text any version
control system you are comfortable with should work fine.
Org-mode is open source.
Org-mode also can be set to display inline images, so even though the
actual .org file stays in plain text for VCS, when you open the file
in Org-mode you can view the images, and comment on them accordingly.
While the .org files themselves are plain text, Org-mode has a number
of export options, including LaTeX, PDF, HTML, DocBook, OpenDocument
and others. So if you want to turn your research notebook into
something more visually appealing than a plain text file, there are
many options. I would recommend this paper for a good description of what Org-mode can do in a research environment.
The downside is that it is a mode for Emacs. If you are not already
using Emacs it has a steep learning curve and can require extensive
customization to get things running exactly the way you want.
Org-mode and AUCTeX (the Emacs LaTeX mode) are the reasons I spent the
time to learn to work with Emacs and I have not been disappointed.
However, if you are looking to get something up and running quickly
(and are not already familiar with Emacs) it may not be your best