To start off, here are the three main 3DNA sites:

http://www.3dna.net - Official company site, where the world downloads are and home of a very active forum.
http://www.blizzbaby.com - Themeing central, more themes and skies for every world than you can shake a stick at.
http://www.triplehelix.info - Info central, having problems, want to know what's coming, want to see some concept art? Go here and get it all

Below is a list of the main new features:

Free Version Features:
1) Can now copy settings for Media Bay and Applications Bay seperately.
2) Doors can open and close automatically
3) Browser bay now shows whether a panel is currently being updated
4) Hotpots, Media Bay buttons have rollover tooltips and glow
5) Added infotips. These can be turned off separately from the tooltips.
6) Added keyboard shortcuts for sky, theme, world choosers and options
7) ctrl-0 can be used to set your entry point in the world rather than appearing where you left the world. This can be disabled in the user options.
8) Dynamic Skies can now have the length of the day, sunrise and sunset times set.
9) In-scene drag and drop to move pictures, shortcuts and browser panels.
10) Drag and drop to file cabinets supported
11) About 3DNA window shows the registration name and serial number
12) Tip of the Day during loading screen
13) Windowed mode - you can specify the size of the 3DNA Desktop and position like a regular window.
14) On Drag and Drop operations, if 3DNA is not visible, hovering over the Control will bring 3DNA to the foreground
15) The floating Control has two sizes (Large and Small)
16) Problem with poking through ceilings while flying solved.
17) Resolved problems with Shortcut Chooser showing wrong icons in some cases
18) Folder structure in IE Favorites is maintained in Favorites Chooser
19) Various improvements to Shortcut and Favorites Choosers
20) Speakers will mute 3DNA sounds with single click
21) Installer revamped - also checks system hardware to set graphics options.
22) Audio controller now handles WinAmp 3 and Windows Media Player 9
23) Portals are theme-able now (portal0.jpg and portal1.jpg)
24) Rename available on shortcut panels, picture panels and 3D models

Additional Paid Version Features:
1) Dual-banks for Browser, Applications, Pictures
2) Posters can be flipped to a second bank with Pictures instead of Ads
3) Dynamic Skies (moving clouds, sun, moon, sunrise/sunset transitions)
4) Ability to run Paid-only worlds.

Known Issues:

1) The recommended requirements are not fluff as in many other programs, if you don't meet them, it will barely work (if at all). These requirements are as follows:
CPU: 1+ Ghz
RAM: 256+ Mb
Video RAM: 64+ Mb
OS: Windows 2000/XP (98 and Me will probably also work, but make sure you have all the service packs installed)
2) You cannot use CompuServe and 3DNA at the same time.
3) Dynamic skies won't work on a ATI Radeon 9700, however this bug will be fixed very soon and only applies to the paid version.