[Samsung Galaxy Nexus] opticyclic:
I want to make a ROM with Best Of Breed apps in it (Android BOB :)).

I will start with a KitKat ROM (probably PA) then replace all the stock system apps with best of breed apps.

Apps must be free and ideally without ads, or with ads that can be blocked with adaway ;).

If they do have ads they can't be be too intrusive and the app has to be significantly better than alternatives to justify it.

Features are important but if an app causes excessive battery drain it will get bumped from the list.

There might be licensing issues in releasing a ROM with apps from the Play Store but I will address those later.

First I want a working ROM for myself.

I need help making a list of stock applications and the best alternatives.

I'll start with a list of what I have on my phone right now then update the original posts as people make suggestions.

When you make a suggestion please provide a link (you don't have to restrict yourself to the Play Store) and explain why it is better than the current app in that category.

Feel free to add another category if something is missing.

Backup Solution* [URL="https://play.google.com/store/apps/details?id=com.keramidas.TitaniumBackup&hl=en"]Titanium Backup Free[/URL]/[URL="https://play.google.com/store/apps/details?id=uk.co.curlybracket.backup&hl=en"]Parcel[/URL]/[URL="https://play.google.com/store/apps/details?id=com.h3r3t1c.bkrestore&hl=en"]Nandroid Manager[/URL]/[URL="https://play.google.com/store/apps/details?id=com.riteshsahu.CallLogBackupRestore&hl=en"]Call Logs Backup & Restore[/URL]/[URL="https://play.google.com/store/apps/details?id=com.riteshsahu.SMSBackupRestore&hl=en"]SMS Backup & Restore[/URL]
Battery Stats Stock?
Browser [URL="https://play.google.com/store/apps/details?id=jp.ddo.pigsty.HabitBrowser&hl=en"]Habit Browser[/URL]
Calculator Stock?
Calendar Stock?
Camera Stock?
Clock Widget [URL="https://play.google.com/store/apps/details?id=in.vineetsirohi.customwidget&hl=en"]UCCW[/URL]+[URL="https://play.google.com/store/apps/details?id=pseudonym.dev.kjd.circley.free"]Circley Free[/URL]
Contacts Stock?
Daydream [URL="https://play.google.com/store/apps/details?id=cz.mpelant.deskclock&hl=en"]Clock Plus[/URL]
Dialler Stock?
Email (with Exchange support) [URL="https://play.google.com/store/apps/details?id=com.trtf.blue&hl=en"]Type Mail[/URL]
File Manager [URL="https://play.google.com/store/apps/details?id=com.estrongs.android.pop&hl=en"]ES File Manager[/URL]
Gallery Stock?
Keyboard [URL="https://play.google.com/store/apps/details?id=com.cootek.smartinputv5&hl=en"]Touchpal[/URL]
SMS Stock?
Superuser [URL="https://play.google.com/store/apps/details?id=eu.chainfire.supersu&hl=en"]SuperSu[/URL]
Theme [URL="https://play.google.com/store/apps/details?id=com.giuros77.onel.grey&hl=en"]OneL+Grey[/URL]
Video Player [URL="https://play.google.com/store/apps/details?id=org.videolan.vlc&hl=en"]VLC[/URL]

Then some extras

Ad Blocking [URL="https://f-droid.org/repository/browse/?fdid=org.adaway"]AdAway[/URL]
Office [URL="https://play.google.com/store/apps/details?id=cn.wps.moffice_eng&hl=en"]WPS Office[/URL]
Soft phone [URL="https://play.google.com/store/apps/details?id=com.csipsimple&hl=en"]CSipSimple[/URL]
Video Chat [URL="https://play.google.com/store/apps/details?id=com.skype.raider&hl=en"]Skype[/URL]
Wakelocks [URL="https://play.google.com/store/apps/details?id=com.uzumapps.wakelockdetector"]Wakelock Detector[/URL]

* I have multiple backup solutions here as none does everything. Titanium backup is reliable but the free version doesn't do batch restore. Parcel does batch restore but I don't feel 100% confident with it. Nandroid manager can extract from Nandroid backups. Call Logs/SMS backup seems to have to be done by separate apps.