Here are a few affordable comics that have key first appearences that could see an increase in value in the next few years.  Because these are independent releases, these are difficult to come across so the demand is starting to overtake the supply.

Noble Causes: Family Secrets 3
  1st app Invincible
  Current Price $15 - $40
  1st Invincible
  There are two versions of this issue and they both contain the first appearence of Invincible.  Invincible is mentioned every month in Wizard magazine as one of the top 5 independent books.  Also, the movie rights for the character have been sold, so if they make a movie, the price could fly because of the low print run.  These books are tough to find, so if you see a nice copy, grab it and hold onto it! 

Dark Horse Comics Presents 5th Anniversary Special
  1st app Sin City
  Current Price $25 - $75
  1st Sin City
  This has a very low print run and is tough to find.  This contains the first appearence of Frank Miller's Sin City.  Yes, that's the same Sin City from the amazing movie in 2005.  The books read just like the movie (almost scene for scene).  There will be a Sin City 2 in late 2006 / early 2007, and this puppy will skyrocket.

Top Cow Triple Play #1
  1st appearence of Seth Green's "The Freshmen"
  Current Price $1.00 - $2.50
  1st Freshmen
  Seth Green (Scott Evil from Austin Powers) cocreated this comic and it is amazing!  He is shopping it around for a movie deal and is a nice gamble for the price.

Walking Dead #1
  1st appearence of Robert Kirkman's "Walking Dead"
  Current price $30 - $75
  1st Walking Dead
  This is a great book with a small print run.  Wizard picks it as one of the best Independent books every month for good reason.  Every month it gains new readers and every month these issues become harder and harder to find.