Marvel first solicited orders for the first issue of the limited comic series Wolverine And The X-Men: Alpha And Omega with a nice anime related Easter egg on the preview cover. Wolverine's partner/antagonist for the series Quentin Quire, aka telepathic mutant Kid Omega, sported the FLCL "P!" symbol:

Some debate that the "P" is a reference to Piaggio, the manufacturer of the Vespa motorscooter ridden by FLCL heroine Haruko Haruhara, but it's generally accept to refer to rock band The Pillows, who provided the anime's theme songs.

Unfortunately, someone at Marvel (most likely in the legal department) thought better of including the reference before the final version saw print:

Wolverine And The X-Men: Alpha And Omega is written by Eisner Award winner Brian Wood (Demo), in a return to Marvel after an exclusive contract with DC, and illustrated by Mark Brooks and Roland Boschi. Besides Wolverine and Kid Omega, the series features Armor, the Japanese mutant who shows up in Madhouse's X-Men anime

Cover artist Mark Brooks has illustrated his share of tributes to FLCL and other anime before:

via Bleeding Cool