Is there a way to customise bookmark icons in Chrome?

I don't think there's a built in way of customizing the favicon, but you can use a chrome extension called Bookmark Favicon Changer which will let you modify it.

Q: Is there a way to customise bookmark icons in Chrome?

A: Not easily.

Bookmark icons are stored in an SQLite database in ...
%LocalAppData%\Google\Chrome\User Data\Default\Favicons.

The icon images are stored (in png format) in the "image_data" field in "favicon_bitmaps" table. This table is indexed on the "image_id" field (numeric). The "image_id" value can be found in the "icon_mapping" table via the indexed "page_url" field.

Additional notes:
1. sometimes there's more than one image per "image_id" (ie when there are different sized images - eg 16x16px, 32x32px)
2. the Favicons file can't be updated (by external applications) while Chrome is running.