Aside from some very small differences in the tips between them, end mills & 2-flute spiral upcut router bits are identical. If you hold up an upcut spiral router bit to a quality carbide end mill, you will immediately see they have the same helical grind to them. For most operations they are identical, although I prefer end mills because they are truly center cutting. End mills are also much cheaper, even though the carbide in a quality end mill is usually finer than that of a router bit. Don't cheese out buying bargain bits. Quality tools make a difference. Avoid high speed steel (HSS) unless you are cutting certain metals like AL where toughness matters.
You're going to want a few different geometries for most things:
1) Upcut spiral or End mill (ObergBrothers.net, Harvey Tool, OSG, SGS, Micro100, Onsrud)
2) Downcut spiral or 'left hand' end mill (Harvey Tool, OSG etc)
3) Straight flute router bit - (OSG, Centurion, Onsrud, Amana, Onsrud etc)
4) Spiral-O bit (single or 2,3 flute) (HarveyTool, Onsrud etc)
5) Form Cutters V-bits etc - Amana, Freud, Onsrud etc
6) Ball end mills for 3D (same as #1)
When in doubt...try a tool out & see if it works for YOUR application.
-B