After some time, I have found that Tomboy notes works the best. With the dynamic linking, and great search feature it seems to work the best for integration with both projects, personal notes, reminders, and meetings.
Tomboy allows me to sync to the web, more specifically my Ubuntu-One share. I used to use both Dropbox, and Evernote, (still do all the time) but our work firewall is increasingly strict. Since I work and play across multiple computers, and operating systems, this has worked out the best. It's like a personal wiki that follows me around.
I must add however that I tag the notes, as well as indicating which project it is related to.
Additionally, if there are any files or data other then unformatted text that needs to be captured, I still must add it to my Outlook Task (for work, Evernote for everything else) by hand. Keeping track of that is as easy as Wiki-Tagging "[_] Added to Outlook?" so at the end of the day (or week) I just right-click the "[_] Added to Outlook?" note, and select "what links here." I put an X in when it's entered.
I like OneNote, but it's not an option. I STILL write all kinds of things down. Plus take pictures. But for speed, search-ability, and syncing, I use Tomboy notes. ZimWiki looks really cool, but the work stuff needs to be encrypted. Without getting into it, it doesn't play well with PGP. I once used my own home wiki for a while. But had to stop for the same reason. Outlook Journal works well, but I don't like putting too much personal information in the company Exchange server, nor can I access it from anywhere.
I should mention, that I also shamelessly use AutoHotkey in Windows and AutoKey in Linux for shortcuts, text expansion and quick pick menus. This keeps the tags, frequently used lists and formatting all the same.
Thank you so much everyone.