In MeGUI-x264 you will find some custom video profiles in the "Video Profiles" drop down list.
Before starting encoding set the bitrate or quantizer (manually or thru the calculator) and adjust the inloop filter accordingly to your needs/taste: keep it 1;1 or higher for anime/toons (max 3;3) and not higher than x264 defaults (0;0) for movies.

Profiles for maximizing Quality and hit a desired bitrate/filesize (2 or more passes, SLOW encoding, High Profile)
HQ-Slow: Pretty slow but not much. Quality is near the best.
HQ-Slower: Slower than HQ-Slow but it tries to squeeze some more compression thru the use of more reference frames.
HQ-Slowest: Same as HQ-Slower with maximized reference frames number and uses --subme=7 and UMH search options.
HQ-Insane: Same as HQ-Slowest but 3 passes and with -t 2 (full trellis).

Profiles for Common Encoding (2-passes)
CE-Highprofile: Common settings using high profile options (not compatible with QuickTime)
CE-Mainprofile: Common settings using main profile options (not compatible with QuickTime)
CE-QuickTime: Common settings for QuickTime 7 compatibility.
CE-Baseline: Common settings using baseline profile options (100% compatible with QuickTime 7)

Profiles for maximizing Speed and hit a desired bitrate/filesize (1-pass)
1P-Maxspeed: Everything disabled for max encoding speed.
1P-Intermediate: Intermediate settings for average speed and final quality.
1P-Goodquality: Settings for good quality with 1 pass.

Profiles for constant Quality/Quantizer (1-pass)
CQ-Lossless: Lossless encoding.
CQ-ASP_Q2_equiv: Almost the equivalent of MPEG-4 ASP Q2 encoding.
CQ-ASP_Q2_eq(crf): Same as above but with "constant quality" (constant rate factor).

Profiles for Anime/Toons (2 or more passes)
AE-Standard: 2 passes, Main Profile, standard quality.
AE-Goodquality: Slower than AE-Standard, High Profile, higher quality.
AE-Maxquality: Slowest mode, 3 passes and maxed out settings, best quality.

Profiles for Consoles and Portable Devices
PD-PSP: Profile for Sony PSP playback.
PD-Xbox_Hires: Profile for MS XBOX and higher than 512pixels resolution (latest XBMC is needed).
PD-Xbox_LoRes: Profile for MS XBOX and lower than 512pixels resolutions (latest XBMC is needed).
PD-iPod: Profile for iPod Video based on Arstechnica settings.
