Since you asked:

cleven - from maemo5

fennec web browser

hamster file manager(or another powerful, phone specific file manager)

flashlight app for the camera flash

wifi-eye

cut down version of libre-office, made to work with the touch screen.

leafpad

htop, or ideally a good GUI proccess manager

QR barcode scanner

good calculator.

fileroller, or a good archive/compressed archive management tool.(intergration into file manager would be nice)

fMMS(Fral's MMS, asked for by name)

good espeak font end.

sysinfo widget.(like n900)

brightness control widget(like the n900)

IP address + interface widget(like the n900)

good audio subsystem and per interface control pannel. Ability to play sounds into the phone subsystem and record them back.

FTP client, like n900ftp, that also does sftp

sharing back ends for gallery2, and other Open/Free protocol based options(use any server)

weather/app widget

wireshark

Caller ID faker/hider widget(like the n900)

Raw GSM information app, like NetMon

keypassX with a better port of the UI

TrueCrypt, and truecrypt integration. ecryptfs and UI intergration.

metadata scubbers, a good camera app, that can be optionally set up to not record metadata. I think a port of MAT is in order
https://mat.boum.org/

GPSJini from the n900, or another good app for raw GPS information

Google Maps

USB host mode

Detailed battery information and calibration app

PDF+ mobile docs reader

widget to switch off the wifi, and all radios, if not built into the OS, like the n900 has.

theme customizer

TOR + I2P + proxy switcher + vidalia

xchat or other IRC client, mabey some UI smoothing for phones. include things ssl, sasl, and script support like modern IRC clients.

GUI disk and file systemt tools.

plugin interface for networking, to add wired connections, proxies, and VPNs, like NetworkManager on the desktop.


also pluggins for most common VPNs, wired ethernet(via usb), and iodine(DNS tunnelling)

some raw NFC and raw bluetooth hacking/experimenation apps.

voice dialing.

secure delete, with UI support for wiping microSD cards securely, and file manager support for wiping files securely

Dosbox

bleachbit

========COMMAND LINE + INTERNALS==============
terminal emulator + bash + GNU userland.https://mat.boum.org/

command line back end for phone functions, so they can be scripted.

dsniff, aircrack-ng, nmap, tcptraceroute, netcat,hping, telnet, ftp, socat, tar, gzip, compression utills, wget, openssh, ethtool, iptraf, monit, snort, etc...

most common command line apps, for servers

torsocks

sshd + fail2ban + iptables + rkhunter + unhide

support for ext*, btrfs, squashfs, aufs, and the whole range of typical linux filesystems, along with cfdisk, parted, and typical filesystem tools.

crypto modules for the kernel included.(AES,TWOFISH,SERPENT, SHA-whatever)

typical desktop kernel modules

boot menu

=========Comms=============
Conversations and Contacts-
I want the same instant message and email integration from maemo5. I also want OTR and GPG integration with a GOOD, easy to use key manager. I also want the full range of libpurple protocols as a plugin too.

I also want VOIP call integration as well, like the n900 had with skype, but with any voice protocol in libpurple or added on.

USB sync to the desktop - I know its not on the phone, but could you guys write a plugin for using a USB cable to sync to various PIM(personal information management) solutions on the linux desktop:

Evolution and Thunderbird specificly.

This should not be hard. I think something like .ispersonalinformation similar to .ismediaplayer with Banshee/Rythmbox could make this easy to sync information on any removable filesystem without the need for any application specific funk.

I also want to be able to sync GPG and OTR keys from my desktop, to my phone, via a usb cable....Easily.


=========Multi-media==================
This is real big, my n900 also doubles as my mp3 player. my jolla phone, will, double as my mp3 player.

multi use media player that works like an mp3 player, and runs in the background if asked too. It would be GREAT if it had gstreamer support, and played any format gstreamer had.

Also adding support for FM radio into the media player would be awesome. Good support that captures tags, and stores presets, and can jump to a station based on keyboard input.

I wouild also like hardware support for ogg,opus,flac, and mp3, to cut down battery use, for all day music player

it also needs to sync to rhythmbox and banshee like it does on the n900.

edit:

forgot shazzaam, that AR app with all the attractions in it.