Would Obama Win Re-Election While Losing The Senate?

[Mr.Phips]

Highly unlikely.  If Obama is winning reelection, he's probably winning most states where Democrats are in tough contests and that will probably give them enough of a boost to win reelection.  The worst a President's party did when winning reelection was in 1940, when FDR's party lost three seats.  A loss like that would give Democrats a 51-50 majority. 

In 2004, Bush's party won four seats.
In 1996, Clinton's party lost two.
In 1984, Reagan's party lost two.
In 1964, Johnson's party gained two. 
In 1956, neither party gained.
In 1948, Truman's party gained nine.
In 1944, FDR's party lost one.
In 1936, FDR's party gained five.

This amounts to an average gain of one seat.  If Democrats match the average, they will have a 54-46 majority.  This would probably happen by losing Nelson in Nebraska, but beating Brown in New Hampshire and Ensign in Nevada. 

[Mr.Phips]

When Clinton was re-elected in 1996, Republicans picked up several Senate seats.

Republicans picked up two that year. 

[Mr.Phips]

From what I can tell, 1936 is the only case where the President's party was defending a class previously elected in a big favorable wave.

1964, 1940, and 1956 as well.