The quality of --alt-preset standard is excellent.
Mp3gain is also excellent, and especially accurate in Album Gain mode, so I'd say go forth and rip!
%s and %d are specific to EAC's user defined encoder functions. EAC has to tell the encoder which temporary WAV file to read and which temporary MP3 file to write. When the encoder has finished, EAC renames the MP3 file and deletes the WAV file.
EAC will actually replace %s with a bit of text representing the path and filename in question, such as c0123456.wav, when it sends the command to Lame
If you left off the %d, lame would write c0123456.wav.mp3, but EAC would expect to see c0123456.mp3 and then try to rename it, but couldn't find it.
Because %s and %d are not recognised by Lame itself, people don't specify them when saying how they encoded. If you used a ripper other than EAC, you'd use something other than %s and %d.
EAC can also pass other information to Lame, and although I normally use Musepack (mppenc) to encode MPC, not Lame to encode MP3, when I use Lame I also get it to tag my files with title, artist, album, tracknumber, year etc. (For that reason I turn OFF EAC's add id3 tag option, because Lame is doing it for me). It uses id3v1.1 tags when possible, but if any field are over 30 characters (28 for the comment), it'll use id3v2 header-tags instead (which go at the beginning of the file and causes problems for some players). I use Foobar2000 player which can read id3v2 header-tags, but won't write them (it writes ID3v1 and APEv2 tags instead).
In each case, EAC expands the %t or similar into a string of characters such as "Enter The Phoenix" and sends that text to Lame, so it will correctly tag the song.
CODE
--alt-preset standard --tc "EAC secure, lame3.90.3 APS" --ta "%a" --tt "%t" --tl "%g" --ty "%y" --tn "%n" --tg "%m" %s %d
I'd say this is great for ripping almost all your albums, so long as you've set up EAC for secure mode. If you plan on doing a big ripping session, it might be wise to look at the list of offset reference CDs and set your drive offsets, in case you're finicky enough to not be satisfied with tracks that start and ends a few milliseconds to early or too late and cause yourself to go back and re-rip everything. (Most CD pressing plants aren't even that finicky)
The exceptions are albums with no gaps between some of the tracks, such as live albums and DJ mix albums. For these you need gapless ripping. Formats like Musepack and Ogg Vorbis are intrinsically gapless, so there's no problem, but MP3 and MP4/AAC aren't gapless and you might be forced to use them for compatibility with a portable player.
If you absolutely need to use MP3 (e.g. to use on a portable MP3 player) this gets complicated. You can either rip the whole album as one giant MP3 with CUE sheet, but most portables won't then allow jumping or shufffling from track to track, because they don't recognise the CUEsheet so see the album as one long track. The other options involve a hack of some sort to split the MP3 without gaps. You either feed the giant MP3 plus CUEsheet through a program like musicutter, or you encode from a CD image plus CUEsheet using Lame 3.90.3 with cuesheet support, which encodes multiple files without gaps pretty darned well. I posted about this yesterday. With VBR this tends to break the correct track length display and seeking-within-track behaviour in most players. This might not be a problem for you, so it'll be fine.
If you only play on a PC, then mp3splice plugin for Winamp v2.x and foo_nogaps Gapkiller for Foobar2000 will allow albums ripped as standard individual files to play gaplessly with amazingly good quality - but that's not the case for portables.
My preference (because of the gapless problem and because I don't have an MP3 portable) is to use Musepack standard, plus --xlevel to prevent clipping in the encoding. It has proper taggging with built in replaygain tag support, it's gapless and it's even better than Lame APS at sounding identical to the original CD (audible artifacts are even rarer). As a bonus it's faster to encode than LAME APS and produces smaller files too! So I can simply rip all my CDs - live, mix or normal - in the same way:
CODE
--quality 5 --xlevel --artist "%a" --title "%t" --album "%g" --year "%y" --track "%n" --genre "%m" --comment "EAC secure, mppenc1.14 --quality 5 --xlevel" %s %d
The mppenc v1.14 encoder uses different switches to lame such as --artist instead of --ta, but EAC still uses the %a replacement variable to pass the information to the encoder. (I use Foobar2000 to scan each album for ReplayGain info after ripping). Also, for mppenc, it's not strictly necessary to specify %d, but it does no harm.
Although I use mppenc now, there are still albums I haven't re-ripped, and I enjoy them immensely as Lame --alt-preset standard MP3s.