As it seems that I really like writing a lot (in English especially) and writing guides (my job requires a lot of standards), I thought of creating a guide for devs/custom rom makers/stock rom modifiers.
This guide is not something that I want to impose, these are just suggestions and I will also include some known issues around here. So, let's begin.
This can be selected as you wish. Any bootanimation other than the standard one should be fine. Or, if you want, you can provide more animations and a short guide on how to change bootanimation.zip and where.
2. Lock Screen
Removing the HTC Lockscreen will lead to the default android Gingerbread one. Now this one's buggy. Like hell. For example, pull the right slider (the one with the sound control) to change the profile to vibrations. Now you can see that the slider is hanging from the top, pointing to bottom (can be fixed with a phone restart).
3. Missing caller screen when phone is locked
If you have the default lockscreen you will notice that there is no incoming call screen displayed when the phone is locked (that or I removed too much stuff). Keep this in mind.
Even though the default Gingercroissant (too much bread:P) looks black, if you pull the status bar (taskbar) you will notice that it turns back to white-grey (the default HTC Sense/ChaCha) one. Keep this in mind when adding icons/notifications. (picking white icons will render them barely visible)
Most devs/modders prefer to add their most liked applications and integrate them into the ROM (so that you cannot uninstall them from Settings -> Applications -> Manage Applications) :P which kinda sucks since not everyone uses/likes the same stuff (it's called "taste"). Basically I am suggestion to add only SuperUser and let the users install their own apps (Titanium, Messenger, GPS, etc.). For example I have my own Titanium Backup.apk (it's personalized) which I want to install - cannot be installed if Titanium is already present though.
6. Google Sync
Some of us like to have the Google account synchronized with the GMail server and I would suggest leaving the Google Contacts Sync and Calendar Sync in the rom (they can be removed later). It's easier to remove than to search the internet and add them separately.
News, Weather, Mirror, Stocks, News&Weather (Yes, 3 different applications for the same stuff), HTC Likes, HTC Hub, Downloads, Facebook, Peep, Tweeter, GTalk.. There are more, of course (for example I have also removed Live wallpaper stuff since I don't use Live wallpapers, skin picker, skin scanner, profile widget, ringtone widget, and more) and it should be taken into consideration this question: how much is really enough?
8. Link2SD and ext-partitions
Well, since custom roms do allow the use of ext and Link2SD I suggest using them as much as possible.
I do hope that this could help some of you (or mocked by others) but any feedback is welcomed.