(Last update: June 8, 2016)
I like the DIN 32635 standard. It has one character per Arabic letter (so, no weird double double consonants for šaddah) and it’s used in European academic publications. A PDF with the full standard can be downloaded here.
Most letters use normal unaccented characters, but there are a few that are tricky to enter in a relatively normal Western computer setup. Nowadays I use mostly Debian Linux with Xfce4, which relies on Gtk, so some of these characters can be entered using the appropriate Compose sequence. Make sure you have defined your Compose key. In Gnome this can be done through the settings menus. In Xfce4 there’s no graphical tool to set it up, but it’s only a matter of running the following command on a terminal, or, better, putting it in one of the many initialization files (.bashrc, .xinitrc, .xinputrc, etc. I have it on .xinputrc, which is more logical)
setxkbmap -option compose:prsc
Here prsc stands for the PrintScreen key, which in my laptop is conveniently located between the right Ctrl and Alt keys. Use the one that suits you better; more key abbreviations here.
A few others transliteration characters have to be either copied from the system’s character map or entered using their Unicode number. If you have iBus installed in your Linux system (which I recommend if you want to enter text in different languages and scripts), the latter is done normally by holding Shift and Ctrl together while typing ‘u’ and the Unicode number in hexadecimal. Depending on your configuration this might be done differently. I have no clue about how this is done in Windows or Mac.
Here’s a table of the tricky characters together with the Compose sequence and Unicode numbers:
|Arabic||Transliteration||Compose||Unicode in hex|
|ث||Ṯ ṯ||1e6e, 1e6f|
|ج||Ǧ ǧ||cG cg||1e6, 1e7|
|ح||Ḥ ḥ||!H !h||1e24, 1e25|
|خ||Ḫ ḫ||1e2a, 1e2b|
|ذ||Ḏ ḏ||1e0e, 1e0f|
|ش||Š š||cS cs||160, 161|
|ص||Ṣ ṣ||!S !s||1e62, 1e63|
|ض||Ḍ ḍ||!D !d||1e0c, 1e0d|
|ط||Ṭ ṭ||!T !t||1e6c, 1e6d|
|ظ||Ẓ ẓ||!Z !z||1e92, 1e93|
|غ||Ġ ġ||.G .g||120, 121|
السلام عليكم al-salāmu ʿalaykum!