Since version 1.1.0 of hydroxygen, you can simply customize the iconset the way you like most.
I added a simple script which you can run to apply some modifications.

BEFORE STARTING YOUR CUSTOMIZATION, THYPE THIS IN A TERMINAL WINDOW:

sudo rm ~/.icons/hydroxygen/icon-theme.cache

Customizing commands list [items marked with "*" are set by default]:

./change-type.sh dustfolder [change folders' colour into dust]*
./change-type.sh acquamarinefolder [change folders into acquamarine]
./change-type.sh blackfolder [change folders' colour into black]
./change-type.sh bluefolder [change folders' colour into blue]
./change-type.sh brownfolder [change folders' colour into brown]
./change-type.sh darkgrayfolder [change folders' colour into darkgray]
./change-type.sh deviantdarkfolder [change folders' colour into deviantdark]
./change-type.sh deviantlightfolder [change folders' colour into deviantlight]
./change-type.sh grayfolder [change folders' colour into gray]
./change-type.sh greenfolder [change folders' colour into green]
./change-type.sh manillafolder [change folders' colour into manilla]
./change-type.sh orangefolder [change folders' colour into orange]
./change-type.sh pinkfolder [change folders' colour into pink]
./change-type.sh redfolder [change folders' colour into red]
./change-type.sh skybluefolder [change folders' colour into skyblue]
./change-type.sh violetfolder [change folders' colour into violet]
./change-type.sh whitefolder [change folders' colour into white]
./change-type.sh yellowfolder [change folders' colour into yellow]

./change-type.sh oxybluefolder [change folders colour into oxygen blue]
./change-type.sh oxyacquamarinefolder [change folders colour into oxygen acquamarine]
./change-type.sh oxyblackfolder [change folders colour into oxygen black]
./change-type.sh oxygreenfolder [change folders colour into oxygen green]
./change-type.sh oxyorangefolder [change folders colour into oxygen orange]
./change-type.sh oxyredfolder [change folders colour into oxygen red]
./change-type.sh oxyvioletfolder [change folders colour into oxygen violet]
./change-type.sh oxywhitefolder [change folders colour into oxygen white]

./change-type.sh aguafolder [change folders into agua ones]
./change-type.sh miniumfolder [change folders into minium ones]

./change-type.sh pacman [change distributor logo to pacman]
./change-type.sh arch [change distributor logo to arch]
./change-type.sh debian [change distributor logo to debian]
./change-type.sh gentoo [change distributor logo to gentoo]
./change-type.sh fedora01 [change distributor logo to fedora - type 01]
./change-type.sh fedora02 [change distributor logo to fedora - type 02]
./change-type.sh mint [change distributor logo to mint]
./change-type.sh gnewsense [change distributor logo to gnewsense]
./change-type.sh mandriva [change distributor logo to mandriva]
./change-type.sh kde01 [change distributor logo to KDE - type 01]
./change-type.sh kde02 [change distributor logo to KDE - type 02]
./change-type.sh pclos [change distributor logo to PC LinuxOS]
./change-type.sh sabayon [change distributor logo to sabayon]
./change-type.sh slax [change distributor logo to slax]
./change-type.sh slack [change distributor logo to slackware]
./change-type.sh suse [change distributor logo to suse]
./change-type.sh redhat [change distributor logo to red hat]
./change-type.sh ubuntu [change distributor logo to ubuntu]
./change-type.sh kubuntu [change distributor logo to kubuntu]
./change-type.sh xubuntu [change distributor logo to xubuntu]
./change-type.sh ubuntustudio [change distributor logo to ubuntu studio]
./change-type.sh poseidon [change distributor logo to poseidon linux]
./change-type.sh foresight [change distributor logo to foresight]
./change-type.sh vendetta [change distributor logo to v for vendetta one]
./change-type.sh anarchy [change distributor logo to anarchy symbol]

./change-type.sh gnome-orange [change distributor logo to gnome-orange]*
./change-type.sh gnome-circle [change distributor logo to gnome-circle]
./change-type.sh gnome-acquamarine [change distributor logo to gnome-acquamarine]
./change-type.sh gnome-black [change distributor logo to gnome-black]
./change-type.sh gnome-blood [change distributor logo to gnome-blood]
./change-type.sh gnome-blue [change distributor logo to gnome-blue]
./change-type.sh gnome-brown [change distributor logo to gnome-brown]
./change-type.sh gnome-green [change distributor logo to gnome-green]
./change-type.sh gnome-pink [change distributor logo to gnome-pink]
./change-type.sh gnome-red [change distributor logo to gnome-red]
./change-type.sh gnome-skyblue [change distributor logo to gnome-skyblue]
./change-type.sh gnome-violet [change distributor logo to gnome-violet]
./change-type.sh gnome-white [change distributor logo to gnome-white]

./change-type.sh naviblack [change navigation arrows to black]*
./change-type.sh naviwhite [change navigation arrows to white]
./change-type.sh naviblue [change navigation arrows to blue]
./change-type.sh navibrown [change navigation arrows to brown]
./change-type.sh navigray [change navigation arrows to gray]
./change-type.sh navigreen [change navigation arrows to green]
./change-type.sh navimanilla [change navigation arrows to manilla]
./change-type.sh naviorange [change navigation arrows to orange]
./change-type.sh navipink [change navigation arrows to pink]
./change-type.sh navired [change navigation arrows to red]
./change-type.sh naviskyblue [change navigation arrows to skyblue]
./change-type.sh naviviolet [change navigation arrows to violet]
./change-type.sh naviyellow [change navigation arrows to yellow]
./change-type.sh naviminimalblack [change navigation arrows to minimal black]
./change-type.sh naviminimalwhite [change navigation arrows to minimal white]

./change-type.sh logout-skyblue [change logout button colour into skyblue]*
./change-type.sh logout-acquamarine [change logout button colour into acquamarine]
./change-type.sh logout-blue [change logout button colour into blue]
./change-type.sh logout-black [change logout button colour into black]
./change-type.sh logout-brown [change logout button colour into brown]
./change-type.sh logout-green [change logout button colour into green]
./change-type.sh logout-gray [change logout button colour into gray]
./change-type.sh logout-orange [change logout button colour into orange]
./change-type.sh logout-red [change logout button colour into red]
./change-type.sh logout-violet [change logout button colour into violet]
./change-type.sh logout-yellow [change logout button colour into yellow]
./change-type.sh logout-white [change logout button colour into white]
./change-type.sh logout-pink [change logout button colour into pink]

./change-type.sh amule-default [change amule icon to default]*
./change-type.sh amule01 [change amule icon to amule01]
./change-type.sh amule02 [change amule icon to amule02]
./change-type.sh amule03 [change amule icon to amule03]
./change-type.sh exaile-default [change exaile icon to exaile-default]*
./change-type.sh exaile01 [change exaile icon to exaile01]
./change-type.sh exaile02 [change exaile icon to exaile02]
./change-type.sh exaile03 [change exaile icon to exaile03]
./change-type.sh filezilla-default [change filezilla icon to filezilla-default]*
./change-type.sh filezilla01 [change filezilla icon to filezilla01]
./change-type.sh firefox-default [change firefox icon to firefox-default]*
./change-type.sh firefox-original [change firefox icon to firefox-original]
./change-type.sh firefox01 [change firefox icon to firefox01]
./change-type.sh firefox02 [change firefox icon to firefox02]
./change-type.sh firefox03 [change firefox icon to firefox03]
./change-type.sh firefox04 [change firefox icon to firefox04]
./change-type.sh firefox05 [change firefox icon to firefox05]
./change-type.sh firefox06 [change firefox icon to firefox06]
./change-type.sh firefox07 [change firefox icon to firefox07]
./change-type.sh firefox08 [change firefox icon to firefox08]
./change-type.sh firefox09 [change firefox icon to firefox09]
./change-type.sh firefox10 [change firefox icon to firefox10]
./change-type.sh firefox11 [change firefox icon to firefox11]
./change-type.sh firefox12 [change firefox icon to firefox12]
./change-type.sh firefox13 [change firefox icon to firefox13]
./change-type.sh thunderbird-default [change thunderbird icon to thunderbird-default]*
./change-type.sh thunderbird-original [change thunderbird icon to thunderbird-original]
./change-type.sh thunderbird01 [change thunderbird icon to thunderbird01]
./change-type.sh thunderbird02 [change thunderbird icon to thunderbird02]
./change-type.sh thunderbird03 [change thunderbird icon to thunderbird03]
./change-type.sh thunderbird04 [change thunderbird icon to thunderbird04]
./change-type.sh thunderbird05 [change thunderbird icon to thunderbird05]
./change-type.sh thunderbird06 [change thunderbird icon to thunderbird06]
./change-type.sh thunderbird07 [change thunderbird icon to thunderbird07]
./change-type.sh totem-default [change totem icon to totem-default]*
./change-type.sh totem01 [change totem icon to totem01]
./change-type.sh emesene-default [change emesene icon to emesene-default]*
./change-type.sh emesene01 [change emesene icon to emesene01]
./change-type.sh emesene02 [change emesene icon to emesene02]
./change-type.sh emesene03 [change emesene icon to emesene03]
./change-type.sh evolution-default [change evolution icon to default one]*
./change-type.sh evolution01 [change evolution icon to evolution01]
./change-type.sh evolution02 [change evolution icon to evolution02]

./change-type.sh other-default [change other apps icon to default one]*
./change-type.sh other01 [change other apps icon to other01]

./change-type.sh newvolume [change volume icons to new ones]*
./change-type.sh oldvolume [change volume icons to old ones]

./change-type.sh newfind [change edit-find and edit-find-replace icons to new ones]*
./change-type.sh oldfind [change edit-find and edit-find-replace icons to old ones]

./change-type.sh trash-default [change user-trash icon to default one]*
./change-type.sh trash01 [change user-trash icon to user-trash01]
./change-type.sh trash02 [change user-trash icon to user-trash02]
./change-type.sh trash03 [change user-trash icon to user-trash03]

./change-type.sh ooo-default [change openoffice.org icons to default ones]*
./change-type.sh ooo-new [change openoffice.org icons to new ones]

./change-type.sh wicd01 [change wicd default icon to wicd01]
./change-type.sh wicd02 [change wicd default icon to wicd02]

./change-type.sh rhythmbox-default [change rhythmbox icon to default one]*
./change-type.sh rhythmbox01 [change rhythmbox icon to rhythmbox-01]

./change-type.sh fusion-default [change fusion icon to default one]*
./change-type.sh fusion-blue [change fusion icon to blue one]*

./change-type.sh digikam-default [change digikam icon to default one]*
./change-type.sh digikam01 [change digikam icon to digikam01]

./change-type.sh solfege-default [change solfege icon to default one]*
./change-type.sh solfege01 [change solfege icon to solfege01]
./change-type.sh solfege02 [change solfege icon to solfege02]
./change-type.sh solfege03 [change solfege icon to solfege03]
./change-type.sh solfege04 [change solfege icon to solfege04]
./change-type.sh solfege05 [change solfege icon to solfege05]
