Among other pieces of evidence:

1.) This page at B-R.com shows that the current Cleveland Indians evolved from a minor league team that started in Toledo in 1892 and as of 1899 was split between Columbus and Grand Rapids.  www.baseball-reference.com/bullpen/Cleveland_indians
2.) How many players on the 1899 Spiders appeared for the 1901 Cleveland American League team?  Exactly zero.

Yet at the same time the owner of the spiders also owned the St. Louis Browns and out all the players from the spiders on the Browns which is why no spiders were on the Indians a few years later...or Naps or whatever they were called. I'm not arguing the issue--hell I wasn't there and I don't know. But it would be nice if someone with more time on their hands than me did some research with old publications or something.

Is there a link I could read about the history on baseball reference? All I found was a timeline but it was a pretty bare bones one at that.

Even wikipedia's Cleveland Spiders article makes it clear that the franchise only existed until 1899.

en.wikipedia.org/wiki/Cleveland_Spiders


The only confusion from all of these sources seems to come from the ambiguity of this paragraph in the Spiders article:
The Robisons sold the assets of the Spiders team to Charles Somers and John Kilfoyle in 1900.^[2] In 1900, the then-minor American League (previously the Western League) fielded a team called the Cleveland Lake Shores. In 1901, after the American League declared major league status, the team became the Cleveland Blues, and eventually the Cleveland Indians.

But as should be clear from all of these other sources, the teams referred to in this paragraph are not intended to be read as one continuous franchise.  The 1900 minor league team (the Lake Shores) was not in any way a continuation of the Spiders franchise.  

Thanks for the links contrarian. I'll take a look at them soon. The following paragraph is what I read on wikipedia. Some people don't like wikipedia but I've always found it quite useful.

"The Robisons' decision to effectively reduce the Spiders to minor league status, along with other intra-league raiding such as that conducted by the Dodgers and to a lesser extent the Pittsburg Pirates, unwittingly helped pave the way to the National League's loss of its major league monopoly. The 12th-place Spiders were one of four teams contracted out of the National League at the end of the 1899 season (the others were the 11th-place Senators, the ninth-place Louisville Colonels and the fourth-place Baltimore Orioles, who were bankrupt). The 1899 fiasco played a role in the major leagues passing a rule which barred one person from owning controlling interest in two clubs.

The Robisons sold the assets of the Spiders team to Charles Somers and John Kilfoyle in 1900.^[2] In 1900, the then-minor American League (previously the Western League) fielded a team called the Cleveland Lake Shores. In 1901, after the American League declared major league status, the team became the Cleveland Blues, and eventually the Cleveland Indians."

Seems like we found the same paragraph.  That's what got me too.  Like I said, I haven't paged through old newspapers or phoned baseball historians.  And if in WIS the Spiders are not considered part of the indians when it comes to franchise leagues that's fine with me.  I'm just interested in the history of the game.  But as far as I can tell this lineage seems to be the most controversial when in WIS. 

Any other ones that seem to fall into this category?

The fact that there is any controversy about this one is odd.  It's just that one paragraph with a little ambiguity from wikipedia.  Every other source that I can find, either online or in print, makes it very clear that these are 2 different franchises.  There should be no controversy here whatsoever.

An excellent print source is Franklin Lewis's "The Cleveland Indians", part of the terrific Putnam series from the 1940s (they published a volume for every major league team).  Chapters 1-4 detail the history of major league baseball in Cleveland.  Chapter 5 tells the story of the formation of the Indians; there is absolutely no question that the Indians were a brand new major league team, an evolution of the Grand Rapids minor league franchise.  No connection to the Spiders is made or implied.  Direct quote: "The Spiders were gone.  All baseball was gone from Cleveland."

As far as other franchises, I'm surprised there hasn't been more controversy about the decision (made just this past year) by baseball-reference to no longer consider the 1901-02 Baltimore Orioles as part of the modern day Yankees.  For a very long time they were considered 1 continuous franchise; no longer.

What was the reasoning of that decision? Didn't the owner of the Orioles move that team to NY?

No.

http://www.sports-reference.com/blog/2014/07/1901-02-orioles-removed-from-yankees-history/

http://ourgame.mlblogs.com/2012/02/29/the-house-that-mcgraw-built/

The decision to remove the 01-02 Orioles from the Highlanders/Yankees lineage is shaky at best. They needed a team in NY so that the AL could equally claim the NYC "zone of influence" as the NL could, and about 25% of the O's roster played for the Highlanders in '03. The Orioles never ceased operations in the '02 season, although they did forfeit one game because of a power move by a majority investor at the time. Their move to NYC was insisted upon by the leadership of the AL, and they effectively handed over the club's assets and players worthy of making the roster, which is in effect, a transfer from one business entity to another.

Fascinating. Yet, lame they did this to the history of the game.

I know it probably doesn't have anything to do with playing WIS, but I know there was a very early baseball club known as the New York Knickerbockers. Did this team just disband or what happened to them? Does anyone know?

Way before our time - you can read about them here:

http://en.wikipedia.org/wiki/New_York_Knickerbockers

Thanks juice. Interesting reading. Should be required reading for all baseball fans.