Are there any other unique items in TF2 other than Top Notch?

The J.Axer's Dapper Topper, Amber's Rad as All Hell Hat and Uncle Sam are unique. There is only one of each, and they were awarded to the first, second and third place winners in the Propaganda Contest.

Some items were gifted in Self-Made quality to their creators. Where an item was credited to a single creator, the Self-Made version of that is the only one in that quality, although this isn't as truly unique as the item is more widely available in normal quality.

Other than the Top Notch, these are the only one-of-a-kind items in TF2.

Other rare items (fewer than 1,000 awarded) include:

• Highlander tournament medals (no more than 9 of each, except for participant medals)
  • Gamers with Jobs tournament (1st, 2nd, and participant medal)
  • ETF2L Highlander tournament (1st, 2nd, 3rd and participant medal)
  • UGC Highlander tournament (1st, 2nd and 3rd for each of Platinum, Silver and Iron divisions, and a participant medal)
• the Saxxy (35 awarded)
• the Golden Wrench (101 awarded, of which no more than 82 still exist)
• the Polycount Pin (92 awarded)
• the Wiki Cap (112 awarded to date)
• the Hat of Undeniable Wealth and Respect (622 still exist)
• Valve weapons (available to Valve staff only)

I guess it somewhat depends on how "unique" an item has to be. For instance, there are certain versions of weapons that are given to key community members, or to the person who actually created the item. Valve employees also have a special class of weapon that is reserved for them. There's a page on the TF2Wiki that describes these and links to some lists.

There's also the weapons made of Australium, including the Golden Wrench and the Saxxy, of which there are very, very few.