One likely point of conflict: the consumer financial protection agency. The House bill calls for a standalone agency, while Dodd has housed his in the Federal Reserve. Senate Republicans, though, want to rein in the scope of its rule-making authority, and give it the power to pre-empt stronger state laws. The White House and most Democrats are strongly opposed, but if the GOP prevails that could cause a bit of a dustup when the House and Senate bills are merged.
Similarly, the House bill calls for an audit of the Federal Reserve, which during the crisis purchased huge numbers of toxic assets from failing institutions. The Senate bill is mostly silent on this score.
By contrast, the Senate seems poised to adopt a stronger set of derivative trading regulations than the House did, but House Financial Services Committee Chairman Barney Frank has acknowledged that his bill should have been stronger on that score, and its unlikely that the House--generally more progressive than the Senate--will object.
In the end, the biggest point of contention may end up being procedural. Frank and House Speaker Nancy Pelosi want the bills to be merged through a formal conference committee (Frank has even said he wants the conference committee to be televised, to put the House GOP on the spot when they object to key, popular aspects of the proposal). But the White House and Senate could decide that it would be easier for the House to take up the Senate bill and wrap up the legislative process by ping ponging the bill back and forth between the two chambers until they agree on a final version.
House Republicans in the meantime have maintained since December a united front against Democratic financial reformlegislation. This week, as Senate negotiations between the two parties resumed, they addressed the possibility that their colleagues in the Senate may send back a bill that received some bipartisan support, saying that if it followed a framework supported by President Obama, they'd vote against it en masse.
In the end, though, if a substantial number of Senate Republicans end up supporting a bill, merging it with the House legislation shouldn't be a terribly heavy lift for Pelosi -- and there's a decent chance some House Republicans will cross over.