Hi!
I have enjoyed a lot pd-extended on windows last year, took a break and switched to Linux (Mint 17.2) a few month ago.
I'm curently using KXStudio repositories for all the audio ecosystem (a great project btw) so I have things like Jack, low latency kernel, etc.
I want to get back to Pure Data but I don't know which version I should use:

• Vanilla PD 0.45.4-1 provided in the Ubuntu repositories (+ libraries if needed)
• Vanilla PD 0.46.7 compiled from sources (+ libraries if needed)
• PD extended 0.43.4 from apt.puredata.info repository (+ updating libraries if needed)
• PD extended 0.44

PD extended seems unmaintained and while I was glad to find anything nicely packaged for Windows, I'm not affraid of compiling things in Linux. What would you recommand me?

The main factor to consider here is what functions you want/need. A basic start there would be to check the Vanilla change log at:

http://msp.ucsd.edu/Pd_documentation/x5.htm#s1

For my own purposes, I have pretty much given up on Extended and now use the latest Vanilla with the deken plugin if I want to grab any extensions.

However, if you really want a big monolithic distro with everything crammed in there already, I would go for the one you missed -- L2ork:

http://l2ork.music.vt.edu/main/?page_id=56

The latest version is based on Extended 0.44 (I think) but with more features . I occasionally use it for the expanded editing functions (IMHO the best thing about it) or to run other users patches made in Extended. It does have it's own quirks and can be a bit wonky sometimes (just like Extended) but again that may depend on individual use, your milleage may vary. It's not too hard to install on any Canonical/Ubuntu based distro (such as Mint) but it gets a bit more tricky with other distros and you may need to consult the mailing list if you are installing it on a different base.

I'd recommend the latest vanilla and if you want external libraries you can install them with apt-get. If you have a 64-bit system and you'll compile vanilla 64-bit, then I guess you'll have to compile any external library yourself, but then, compiling Pd itself and external libraries is not a difficult task on Linux.
The latest vanilla has some really nice new features, like its native OSC objects and the new [array] and [text] objects that are super flexible..

Thanks for the feedback!
As I will work a lot with OSC, and after reading the changelog, I'll go with the latest vanilla and compile whatever I need.

One thing worth mentioning: If you use the "make install" command to install your compiled package (i.e. bypassing the distro's package management) don't try to install any of the other directly Pd related packages in the distro's repository as this will automatically install the older version of Pd from the same repository -- giving you a dual install of Pd with the repo packages only working with the older version.

It's for this reason that I switched to using the "checkinstall" program to create a puredata .deb file to replace the old version in the distro's package management.

I use checkinstall whenever I can, I find this easier for keeping a clean system