Best way to thank little sister (present ideas)

Have your OH give her a special mention/toast in his speech. My mum made our wedding cake and my husband toasted her which she was really touched with. She didn't expect it at all! We also gave her a solid silver picture frame with a line from our (personalised) vows engraved along the top and a voucher from our photographer so she could chose a picture to put in it and not have to pay for it!

It might be a bit 'grown up' as I don't know how old your sister is!

Thanking her during the speeches is a lovely idea. And maybe you could get her something baking related if she's a keen baker?

I love these figurines. I got this one for my sister as a thank you gift.

http://www.amazon.co.uk/Willow-Tree-Sisters-Heart-Figurine/dp/B001329JVU/ref=sr_1_34?ie=UTF8&qid=1333267913&sr=8-34

Or, if you want something more personal, how about making some jewellery for her? If she already makes her own then she'll understand the work you put into it and really appreciate the gesture?

I've bought my bridesmaids (which includes my sister) Irregular Choice clutch bags. They all love IC products, it's a bit of a 'splash out' that they wouldn't treat themselves to, it's less predictable than jewellery, it's something to keep, and hugely functional on the day and beyond.