Right click project in project explorer window, choose "Export...", then choose "Deployable plug-ins and fragments" under "Plug-in Development". After that everything should be simple - when choosing directory to export be aware that inside that directory plugins subdirectory will be created and plugin jar will be placed in it (rather than in directory itself).

Run pkg clean. Quite logical, but I keep forgetting command.

Run cert-sync --user /etc/ssl/cert.pem. Omit --user to synchronize for entire system (note that this installs them in /usr/share/.mono rather than /usr/local/share/.mono).

Without this you might be experiencing errors like "Ssl error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED" or similar

Reason for this is application .desktop file missing MimeType specification. For example for me mplayer and thunderbird are not listed as choices for video and mail respectively. To fix this edit application's .desktop file (in /usr/local/share/applications directory, or in ~/.local/share/applications) and run update-desktop-database afterwards (with -v to show its warnings).

To get list of manually installed packages (ie, those not installed as dependencies) use this command:
pkg query -e '%a = 0' %o | sort

In case normal unzip can't handle them properly (I was unable to make it do it properly) use 7 zip instead (package p7zip) - command to use is
7z x path_to_zip

Quite useful tutorial for making timelapse.

Obviously plugin has to be enabled when building IcedTea. Apparently some systems (like iLo) can't use java web start with OpenJDK. For them applets have to be used but by default they won't open in Firefox - for iLo to work without surprises it is necessary to choose "always activate" for java plugin (Tools > Add-ons > Plugins, then find IcedTea-Web and choose "Always Activate" for it).

TLS 1.2 is not enabled in default version of Mono 4.8.1 port for FreeBSD.

One place to put all little tweaks to make it work better with FreeBSD.